Miracle-dz/UniFAR-FTUs huggingface dataset:
Deception and Manipulation: The Arms of Leishmania, a Successful Parasite

Leishmania spp. are intracellular parasitic protozoa responsible for a group of neglected tropical diseases, endemic in 98 countries around the world, called leishmaniasis. These parasites have a complex digenetic life cycle requiring a susceptible vertebrate host and a permissive insect vector, which allow their transmission. The clinical manifestations associated with leishmaniasis depend on complex interactions between the parasite and the host immune system. Consequently, leishmaniasis can be manifested as a self-healing cutaneous affliction or a visceral pathology, being the last one fatal in 85–90% of untreated cases. As a result of a long host–parasite co-evolutionary process, Leishmania spp. developed different immunomodulatory strategies that are essential for the establishment of infection. Only through deception and manipulation of the immune system, Leishmania spp. can complete its life cycle and survive. The understanding of the mechanisms associated with immune evasion and disease progression is essential for the development of novel therapies and vaccine approaches. Here, we revise how the parasite manipulates cell death and immune responses to survive and thrive in the shadow of the immune system.
Type 1 Inositol 1,4,5-Trisphosphate Receptor Is Required for Induction of Long-Term Depression in Cerebellar Purkinje Neurons

The inositol 1,4,5-trisphosphate receptor (InsP3R) is an intracellular Ca2+ channel that releases Ca2+ from internal Ca2+ stores in response to InsP3. Although InsP3R is highly expressed in various regions of the mammalian brain, the functional role of this receptor has not been clarified. We show here that cerebellar slices prepared from mice with a disrupted InsP3R type 1 gene, which is predominantly expressed in Purkinje cells, completely lack long-term depression (LTD), a model of synaptic plasticity in the cerebellum. Moreover, a specific antibody against InsP3R1, introduced into wild-type Purkinje cells through patch pipettes, blocked the induction of LTD. These data indicate that, in addition to Ca2+ influx through Ca2+ channels on the plasma membrane, Ca2+ release from InsP3R plays an essential role in the induction of LTD, suggesting a physiological importance for InsP3R in Purkinje cells.
Integration of analytic network process with service measurement index framework for cloud service provider selection

The growing popularity of cloud services has attracted large number of business organizations to enter into the cloud market. The varied availability of cloud service providers, for various services, leaves the cloud customers into skepticism. Service measurement index (SMI) framework, which is based on the analytic hierarchical process, is developed for the ranking of cloud services. As there are multiple dependencies among the criteria for the selection of cloud service provider, analytic hierarchical process formulation is not efficient. In the proposed work, analytic network process that captures the cloud service‐provider selection problem in a more realistic way is integrated in the ranking component of SMI framework. In this method, interactions among the criteria are used for the ranking of the cloud services. Few new criterions are also added into the existing SMI framework to make the framework more effective. A case study is conducted to analyze the proposed technique for the cloud provider selection.
Risk and Reward Are Processed Differently in Decisions Made Under Stress

Years of research have shown that stress influences cognition. Most of this research has focused on how stress affects memory and the hippocampus. However, stress also affects other regions involved in cognitive and emotional processing, including the prefrontal cortex, striatum, and insula. New research examining the impact of stress on decision processes reveals two consistent findings. First, acute stress enhances selection of previously rewarding outcomes but impairs avoidance of previously negative outcomes, possibly due to stress-induced changes in dopamine in reward-processing brain regions. Second, stress amplifies gender differences in strategies used during risky decisions, as males take more risk and females take less risk under stress. These gender differences in behavior are associated with differences in activity in the insula and dorsal striatum, brain regions involved in computing risk and preparing to take action.
Annotating Needles in the Haystack without Looking: Product Information Extraction from Emails

Business-to-consumer (B2C) emails are usually generated by filling structured user data (e.g.purchase, event) into templates. Extracting structured data from B2C emails allows users to track important information on various devices. However, it also poses several challenges, due to the requirement of short response time for massive data volume, the diversity and complexity of templates, and the privacy and legal constraints. Most notably, email data is legally protected content, which means no one except the receiver can review the messages or derived information. In this paper we first introduce a system which can extract structured information automatically without requiring human review of any personal content. Then we focus on how to annotate product names from the extracted texts, which is one of the most difficult problems in the system. Neither general learning methods, such as binary classifiers, nor more specific structure learning methods, suchas Conditional Random Field (CRF), can solve this problem well. To accomplish this task, we propose a hybrid approach, which basically trains a CRF model using the labels predicted by binary classifiers (weak learners). However, the performance of weak learners can be low, therefore we use Expectation Maximization (EM) algorithm on CRF to remove the noise and improve the accuracy, without the need to label and inspect specific emails. In our experiments, the EM-CRF model can significantly improve the product name annotations over the weak learners and plain CRFs.
Fixed‐ or Controlled‐Dose Mycophenolate Mofetil with Standard‐ or Reduced‐Dose Calcineurin Inhibitors: The Opticept Trial

Mycophenolate mofetil (MMF) was developed with cyclosporine as a fixed‐dose immunosuppressant. More recent data indicate a relationship between mycophenolic acid (MPA) exposure in individuals and clinical endpoints of rejection and toxicity. This 2‐year, open‐label, randomized, multicenter trial compared the efficacy and safety of concentration‐controlled MMF (MMFCC) dosing with a fixed‐dose regimen in 720 kidney recipients. Patients received either (A) MMFCC and reduced‐level calcineurin inhibitor (MMFCC/CNIRL); (B) MMFCC and standard‐level CNI (MMFCC/CNISL); or (C) fixed‐dose MMF and CNISL (MMFFD/CNISL). Antibody induction and steroid use were according to center practice. The primary endpoint was noninferiority (α= 0.05) of group A versus group C for treatment failure (including biopsy‐proven acute rejection [BPAR], graft loss and death) at 1 year. Although mean CNI trough levels in group A did not reach the prespecified targets, they were statistically lower than those in groups B and C (p ≤ 0.01 for each comparison). BPAR rates (8.5%) were low across groups. Group A had 19% fewer treatment failures (23% vs. 28%, p = 0.18). MMF doses were highest (p < 0.05), with withdrawals for adverse events the fewest (p = 0.02), in group A. Of the 80% of subjects taking tacrolimus (Tac), those with higher MPA exposure had significantly less rejection (p < 0.001) and diarrhea correlated with Tac, but not with MPA levels. Thus, MMFCC with low‐dose CNI resulted in outcomes not inferior to those with standard CNI exposure and MMFFD, indicating potential utility of MMFCC in CNI‐sparing regimens.
Quality of mango nectar processed by high-pressure homogenization with optimized heat treatment.

UNLABELLED This work aimed to evaluate the effect of high-pressure homogenization (HPH) with heat shock on Aspergillus niger, vitamin C, and color of mango nectar. The nectar was processed at 200 MPa followed by heat shock, which was optimized by response surface methodology by using mango nectar ratio (45 to 70), heat time (10 to 20), and temperature (60 to 85 °C) as variables. The color of mango nectar and vitamin C retention were evaluated at the optimized treatments, that is, 200 MPa + 61.5 °C/20 min or 73.5 °C/10 min. The mathematical model indicates that heat shock time and temperature showed a positive effect in the mould inactivation, whereas increasing ratio resulted in a protective effect on A. niger. The optimized treatments did not increase the retention of vitamin C, but had positive effect for the nectar color, in particular for samples treated at 200 MPa + 61.5 °C/20 min. PRACTICAL APPLICATION The results obtained in this study show that the conidia can be inactivated by applying HPH with heat shock, particularly to apply HPH as an option to pasteurize fruit nectar for industries.
Role of Conserved Histidine Residues in the Low-pH Dependence of the Semliki Forest Virus Fusion Protein

ABSTRACT A wide variety of enveloped viruses infects cells by taking advantage of the low pH in the endocytic pathway to trigger virus-membrane fusion. For alphaviruses such as Semliki Forest virus (SFV), acidic pH initiates a series of conformational changes in the heterodimeric virus envelope proteins E1 and E2. Low pH dissociates the E2/E1 dimer, releasing the membrane fusion protein E1. E1 inserts into the target membrane and refolds to a trimeric hairpin conformation, thus driving the fusion reaction. The means by which E1 senses and responds to low pH is unclear, and protonation of conserved E1 histidine residues has been proposed as a possible mechanism. We tested the role of four conserved histidines by mutagenesis of the wild-type (wt) SFV infectious clone to create virus mutants with E1 H3A, H125A, H331A, and H331A/H333A mutations. The H125A, H331A, and H331A/H333A mutants had growth properties similar to those of wt SFV and showed modest change or no change in the pH dependence of virus-membrane fusion. By contrast, the E1 H3A mutation produced impaired virus growth and a markedly more acidic pH requirement for virus-membrane fusion. The dissociation of the H3A heterodimer and the membrane insertion of the mutant E1 protein were comparable to those of the wt in efficiency and pH dependence. However, the formation of the H3A homotrimer required a much lower pH and showed reduced efficiency. Together, these results and the location of H3 suggest that this residue acts to regulate the low-pH-dependent refolding of E1 during membrane fusion.
Learning Cross-lingual Representations with Matrix Factorization

We present a matrix factorization model for learning cross-lingual representations. Using sentence-aligned corpora, the proposed model learns distributed representations by factoring the given data into language-dependent factors and one shared factor. Moreover, the model can quickly learn shared representations for more than two languages without undermining the quality of the monolingual components. The model achieves an accuracy of 88% on English to German cross-lingual document classiﬁcation, and 0.8 Pearson correlation on Spanish-English cross-lingual semantic textual similarity. While the results do not beat state-of-the-art performance in these tasks, we show that the crosslingual models are at least as good as their monolingual counterparts.
ClEPaps: Fast Pair Alignment of protein Structures Based on conformational Letters

Fast, efficient, and reliable algorithms for pairwise alignment of protein structures are in ever-increasing demand for analyzing the rapidly growing data on protein structures. CLePAPS is a tool developed for this purpose. It distinguishes itself from other existing algorithms by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of the three angles formed by Calpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. CLePAPS regards an aligned fragment pair (AFP) as an ungapped string pair with a high sum of pairwise CLESUM scores. Using CLESUM scores as the similarity measure, CLePAPS searches for AFPs by simple string comparison. The transformation which best superimposes a highly similar AFP can be used to superimpose the structure pairs under comparison. A highly scored AFP which is consistent with several other AFPs determines an initial alignment. CLePAPS then joins consistent AFPs guided by their similarity scores to extend the alignment by several "zoom-in" iteration steps. A follow-up refinement produces the final alignment. CLePAPS does not implement dynamic programming. The utility of CLePAPS is tested on various protein structure pairs.
Learning Together and Alone. Cooperative, Competitive, and Individualistic Learning. Fourth Edition.

Preface. 1.Cooperative, Competitive, and Individualistic Learning. 2.Cooperative Learning. 3.Informal Cooperative Learning. 4.Cooperative Base Groups. 5.Basic Elements of Cooperative Learning. 6.Integrated Use of All Types of Cooperative Learning. 7.Assessment and Evaluation. 8.Structuring Competitive Learning. 9.Structuring Individualistic Learning. 10.Integrated Use of Cooperative, Competitive, and Individualistic Learning. 11.Reflections. Glossary. References. Index.
Health-related quality of life in patients with idiopathic pulmonary fibrosis: a systematic review

Background: Idiopathic pulmonary fibrosis (IPF) profoundly affects the quality of patients’ lives. A systematic review was performed to evaluate critically the published literature and to examine what is known about health-related quality of life (HRQL) in patients with IPF. Methods: The MEDLINE, EMBASE, Health and Psychosocial Instruments, and Cochrane Library databases were searched to 1 April 2004. Abstracts and bibliographies of published articles were scanned and contact was made with investigators. Included studies analysed HRQL (or quality of life) in at least 10 patients with IPF. Two reviewers independently selected studies, evaluated their quality according to predetermined criteria, and abstracted data on study design, patients’ demographic and clinical characteristics, and quality of life outcome measures. Results: Seven studies met the inclusion criteria. The studies enrolled 512 patients with IPF and used three different instruments to measure HRQL. All studies had important limitations in methodological quality; none measured longitudinal changes in HRQL over time. Patients reported substantially impaired HRQL, especially in domains that measured physical health and level of independence. Patients with IPF appear to have similar impairments in HRQL to those with chronic obstructive pulmonary disease. Measures of dyspnoea were moderately correlated with scores from domains that measured physical health (R2 = 0.03–0.66) and energy/fatigue/pep (R2 = 0.19–0.55), but measures of pulmonary function and gas exchange did not correlate as strongly with these and other domains. Conclusion: Studies of HRQL in patients with IPF suggest that, in addition to the obvious effect on physical health, general health, energy level, respiratory symptoms, and level of independence are also impaired. Variability in HRQL among patients is not fully explained by measures of dyspnoea or pulmonary function, suggesting that HRQL measures provide unique information. More research is needed to identify or design appropriate measurement instruments for patients with IPF and to examine changes in HRQL over time or in response to specific treatments.
Structured Admission Control Policy in Heterogeneous Wireless Networks with Mesh Underlay

In this paper, we investigate into optimal admission control policies for Heterogeneous Wireless Networks (HWN), considering an integration of wireless mesh networks with an overlaying cellular infrastructure. In order to characterize the overflow traffic from the underlaying mesh to the overlay, a Partially-Observable Markov-Modulated Poisson Process (PO-MMPP) traffic model is developed. This model captures the burstiness of the overflow traffic under the imperfect observability of the mesh network states. Then, by modeling the overlay network as a controlled PO-MMPP/M/C/C queueing system and obtaining structured decision theoretic results, it is shown that the optimal control policies for this class of HWNs can be characterized as monotonic threshold curves. Further, these results are used to design a computationally efficient algorithm to determine the optimal policy in terms of thresholds. Numerical observations suggest that the proposed algorithm is efficient in terms of time-complexity and can drastically reduce the cost of dropped and blocked calls.
Change agency in a primary health care context: The case of distributed leadership

Background: Integration of services across disciplines and organizations has been pursued increasingly in the primary care sector. Successful integration requires adept leadership of change. There have been questions about the extent to which studies on change agency that focus on a stand-alone leader are applicable in the complex setting of health care. It has been suggested that a model of collective leadership is more appropriate to this setting. Purpose: The objective is to understand the dynamics of collective or distributed leadership by attending to change agency roles in a context involving collaboration across health organizations. The study examines how change agency roles develop, evolve, interact, and complement each other. It also examines the bases of the change agents' ability to exercise influence. Methodology: A qualitative, longitudinal case study allowed us to map the evolution of a successful model of leadership. We tracked changes and agents' roles by engaging in extensive observations and conducting 74 interviews over a period of 4 years. Findings: The findings point to the importance of the distributed change leadership model in contexts where legitimacy, authority, resources, and ability to influence complex change are dispersed across loci. Distributed leadership has both planned and emergent components, and its success in bringing about change is associated with the social capital prevalent in the site. Practice Implications: Change leaders need to build a winning coalition of agents with complementary skills and resources that support the change. Successful change leadership involves investing time in finding common ground across stakeholders and in building credibility and trust. Having an agent whose main responsibility is to manage the change process is likely to bring more success than asking busy health care practitioners to take on this charge because in the latter case, there is likelihood of dilution of change focus and momentum.
In search of path diversity in ISP networks

Internet Service Providers (ISPs) can exploit path diversity to balance load and improve robustness. Unfortunately, it is difficult to evaluate the potential impact of these approaches without routing and topological data, which are confidential. In this paper, we characterize path diversity in the real Sprint network. We then characterize path diversity in ISP topologies inferred using the Rocketfuel tool. Comparing the real Sprint topology to the one inferred by Rocketfuel, we find that the Rocketfuel topology has significantly higher apparent path diversity. (As a metric, path diversity is particularly sensitive to the presence of false or missing links, both of which are artifacts of active measurement techniques.) We evaluate heuristics that improve the accuracy of the inferred Rocketfuel topologies. Finally, we discuss limitations of active measurements techniques to capture topological properties such as path diversity.
Genome-Wide Association Study of L-Arginine and Dimethylarginines Reveals Novel Metabolic Pathway for Symmetric Dimethylarginine

Background—Dimethylarginines (DMA) interfere with nitric oxide formation by inhibiting nitric oxide synthase (asymmetrical DMA [ADMA]) and L-arginine uptake into the cell (ADMA and symmetrical DMA [SDMA]). In prospective clinical studies, ADMA has been characterized as a cardiovascular risk marker, whereas SDMA is a novel marker for renal function and associated with all-cause mortality after ischemic stroke. The aim of the current study was to characterize the environmental and genetic contributions to interindividual variability of these biomarkers. Methods and Results—This study comprised a genome-wide association analysis of 3 well-characterized population-based cohorts (Framingham Heart Study [FHS; n=2992], Gutenberg Health Study [GHS; n=4354], and Multinational Monitoring of Trends and Determinants in Cardiovascular Disease Study [MONICA]/Cooperative Health Research in the Augsburg Area, Augsburg, Bavaria, Germany [KORA] F3 [n=581]) and identified replicated loci (DDAH1, MED23, Arg1, and AGXT2) associated with the interindividual variability in ADMA, L-arginine, and SDMA. Experimental in silico and in vitro studies confirmed functional significance of the identified AGXT2 variants. Clinical outcome analysis in 384 patients of the Leeds stroke study demonstrated an association between increased plasma levels of SDMA, AGXT2 variants, and various cardiometabolic risk factors. AGXT2 variants were not associated with poststroke survival in the Leeds study or were they associated with incident stroke in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Conclusions—These genome-wide association study support the importance of DDAH1 and MED23/Arg1 in regulating ADMA and L-arginine metabolism, respectively, and identify a novel regulatory renal pathway for SDMA by AGXT2. AGXT2 variants might explain part of the pathogenic link between SDMA, renal function, and outcome. An association between AGXT2 variants and stroke is unclear and warrants further investigation.
Language Learning and Deafness: Language varieties in the deaf population and their acquisition by children and adults

Editor's introduction In this chapter, Bochner and Albertini take on the ambitious task of reviewing the central issues in the acquisition of language by deaf individuals in North America. They adopt a self-described “sociolinguistic” perspective by viewing language acquisition by the deaf as occurring under conditions of restricted intake that result in learning patterns resembling those of pidgin and Creole speakers . In order to explore this analogy in depth, the authors first provide an overview of research on the “products” or linguistic output of deaf learners, including written and spoken English, manual English, Pidgin Sign English (PSE), and American Sign Language (ASL). They then consider various aspects of the acquisition process, particularly those related to the interplay between the organism and the environment, the relationship between communication channel and the mind, and the influence of age on intake . Apart from the thoroughness with which Bochner and Albertini treat their topic, what makes this chapter an important contribution to applied linguistics is their insights on the relationship between language acquisition among the Deaf and among other speech communities and the implications they draw from the linguistic evidence for the education of deaf children. The importance of primary language acquisition (whether ASL or signed or spoken English) and of the quality of language input/intake for educational advancement is lent an added urgency by the evidence and arguments put forward by these authors.