Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring immune system variation to help understand host-pathogen community dynamics

SUMMARY Carefully chosen immunological measurements, informed by recent advances in our understanding of the diversity and control of immune mechanisms, can add great interpretative value to ecological studies of infection. This is especially so for co-infection studies, where interactions between species are often mediated via the host's immune response. Here we consider how immunological measurements can strengthen inference in different types of co-infection analysis. In particular, we identify how measuring immune response variables in field studies can help reveal inter-species interactions otherwise obscured by confounding processes operating on count or prevalence data. Furthermore, we suggest that, due to the difficulty of quantifying microbial pathogen communities in field studies, innate responses against broad pathogen types (mediated by pattern response receptors) may be useful quantitative markers of exposure to bacteria and viruses. An ultimate goal of ecological co-infection studies may also be to understand how dynamics within host-parasite assemblages emerge from trade-offs involving different arms of the immune system. We reflect on the phenotypic measures that might best represent levels of responsiveness and bias in immune function. These include mediators associated with different T-helper cell subsets and innate responses controlled by pattern response receptors, such as the Toll-like receptors (TLRs).
Joint Stochastic Approximation learning of Helmholtz Machines

Though with progress, model learning and performing posterior inference still remains a common challenge for using deep generative models, especially for handling discrete hidden variables. This paper is mainly concerned with algorithms for learning Helmholz machines, which is characterized by pairing the generative model with an auxiliary inference model. A common drawback of previous learning algorithms is that they indirectly optimize some bounds of the targeted marginal log-likelihood. In contrast, we successfully develop a new class of algorithms, based on stochastic approximation (SA) theory of the Robbins-Monro type, to directly optimize the marginal log-likelihood and simultaneously minimize the inclusive KL-divergence. The resulting learning algorithm is thus called joint SA (JSA). Moreover, we construct an effective MCMC operator for JSA. Our results on the MNIST datasets demonstrate that the JSA's performance is consistently superior to that of competing algorithms like RWS, for learning a range of difficult models.
New CycloAMB-Nucleoside Phosphonate Prodrugs

cycloSal- and cycloAmb-nucleoside phosphonate prodrugs of PMEA were synthesized and characterized. Each of these compounds showed different disadvantages in hydrolysis. Thus, a new series of cycloAminobenzyl(cycloAmb)-PMEA prodrugs was synthezised and studied with regard to their hydrolysis properties and biological activity.
The importance of critically interpreting simulation studies.

such studies. As we discuss here, it is nearly impossible to capture all potentially relevant aspects of a real study with a simulation; as a consequence, simulation results have limited generalizability. Simulation results also may suffer from programming error, rounding error, algorithmic error, and random error. These problems reveal the danger of overgeneralizing from simulation results and the importance of viewing simulation studies as analogous to clinical trials (which demand corroboration and cautious interpretation), rather than as definitive math? ematical studies.
Leveraging SDN to monitor critical infrastructure networks in a smarter way

In critical infrastructures, communication networks are used to exchange vital data among elements of Industrial Control Systems (ICSes). Due to the criticality of such systems and the increase of the cybersecurity risks in these contexts, best practices recommend the adoption of Intrusion Detection Systems (IDSes) as monitoring facilities. The choice of the positions of IDSes is crucial to monitor as many streams of data traffic as possible. This is especially true for the traffic patterns of ICS networks, mostly confined in many subnetworks, which are geographically distributed and largely autonomous. We introduce a methodology and a software architecture that allow an ICS operator to use the spare bandwidth that might be available in over-provisioned networks to forward replicas of traffic streams towards a single IDS placed at an arbitrary location. We leverage certain characteristics of ICS networks, like stability of topology and bandwidth needs predictability, and make use of the Software-Defined Networking (SDN) paradigm. We fulfill strict requirements about packet loss, for both functional and security aspects. Finally, we evaluate our approach on network topologies derived from real networks.
Optimal rewards in multiagent teams

Following work on designing optimal rewards for single agents, we define a multiagent optimal rewards problem (ORP) in common-payoff (or team) settings. This new problem solves for individual agent reward functions that guide agents to better overall team performance relative to teams in which all agents guide their behavior with the same given team-reward function. We present a multiagent architecture in which each agent learns good reward functions from experience using a gradient-based algorithm in addition to performing the usual task of planning good policies (except in this case with respect to the learned rather than the given reward function). Multiagency introduces the challenge of nonstationarity: because the agents learn simultaneously, each agent's learning problem is nonstationary and interdependent on the other agents. We demonstrate on two simple domains that the proposed architecture outperforms the conventional approach in which all the agents use the same given team-reward function (even when accounting for the resource overhead of the reward learning); that the learning algorithm performs stably despite the nonstationarity; and that learning individual reward functions can lead to better specialization of roles than is possible with shared reward, whether learned or given.
Development and Persistence of Antimicrobial Resistance in Pseudomonas aeruginosa: a Longitudinal Observation in Mechanically Ventilated Patients

ABSTRACT Intubated patients frequently become colonized by Pseudomonas aeruginosa, which is subsequently responsible for ventilator-associated pneumonia. This pathogen readily acquires resistance against available antimicrobials. Depending on the resistance mechanism selected for, resistance might either be lost or persist after removal of the selective pressure. We investigated the rapidity of selection, as well as the persistence, of antimicrobial resistance and determined the underlying mechanisms. We selected 109 prospectively collected P. aeruginosa tracheal isolates from two patients based on their prolonged intubation and colonization periods, during which they had received carbapenem, fluoroquinolone (FQ), or combined β-lactam-aminoglycoside therapies. We determined antimicrobial resistance phenotypes by susceptibility testing and used quantitative real-time PCR to measure the expression of resistance determinants. Within 10 days after the initiation of therapy, all treatment regimens selected resistant isolates. Resistance to β-lactam and FQ was correlated with ampC and mexC gene expression levels, respectively, whereas imipenem resistance was attributable to decreased oprD expression. Combined β-lactam-aminoglycoside resistance was associated with the appearance of small-colony variants. Imipenem and FQ resistance persisted for prolonged times once the selecting antimicrobial treatment had been discontinued. In contrast, resistance to β-lactams disappeared rapidly after removal of the selective pressure, to reappear promptly upon renewed exposure. Our results suggest that resistant P. aeruginosa is selected in less than 10 days independently of the antimicrobial class. Different resistance mechanisms lead to the loss or persistence of resistance after the removal of the selecting agent. Even if resistant isolates are not evident upon culture, they may persist in the lung and can be rapidly reselected.
Charismatic computers: creating more likable and persuasive interactive technologies by leveraging principles from social psychology

Following the Computers Are Social Actors (CASA) paradigm, this dissertation investigated the claim that computers will be perceived as more likable and persuasive when they leverage principles and dynamics that make people more likable and persuasive. The first study $(N=68)$ used a 2 x 2 between-subjects design (praise or criticism; contingent or noncontingent evaluation) along with a fifth condition (generic response) to experimentally investigate how users would respond to computers that flattered them. The results show that users responded to unambiguous flattery from computers in the same positive ways that users responded to praise from computers. Among other findings, computers that flattered were perceived to be more likable and to have performed better than computers that provided no evaluations. The second line of research explored responses to computers as teammates. The first experiment $(N=56)$ was a 2 x 2 between-subjects design (identity or no identity; interdependence or no interdependence). The results show consistent main effects for interdependence but no effects for identity. Compared to noninterdependent users, users who were interdependent with the computer found the computer's information to be of higher quality, and they conformed more to the computer's suggestions, among other findings. A follow-up experiment $(N=28)$ manipulated only identity. Those in the identity condition showed significant effects of team affiliation with the computer. The third line of research examined if the rule of reciprocity in human-computer interactions could cause behavior change in users. This experiment $(N=76)$ employed a 2 x 2 design (high help or low help from computer on the first task; same or different computer on the second task). The results show that users reciprocated more help to a computer that had helped them previously than to a different computer. Reciprocity users provided more help to the computer and performed higher quality work for the computer. Users may have retaliated against computers that did not perform well. The findings from these three human-computer studies are consistent with the findings from human-human studies in social psychology. Together these studies demonstrate that theories from social psychology can guide the design of charismatic computers.
Simian Immunodeficiency Virus (SIV) Envelope-Specific Fabs with High-Level Homologous Neutralizing Activity: Recovery from a Long-Term-Nonprogressor SIV-Infected Macaque

ABSTRACT An antibody phage display library was constructed from RNA extracted from lymph node cells of a simian immunodeficiency virus (SIV)-infected long-term-nonprogressor macaque. Seven gp120-reactive Fabs were obtained by selection of the library against SIV monomeric gp120. Although each of the Fabs was unique in sequence, there were two distinct groups based on epitope recognition, neutralizing activity in vitro, and molecular analysis. Group 1 Fabs did not neutralize SIV and bound to a linear epitope in the V3 loop of the SIV envelope. In contrast, two of the group 2 Fabs neutralized homologous, neutralization-sensitive SIVsm isolates with high efficiency but failed to neutralize heterologous SIVmac isolates. Based on competition enzyme-linked immunosorbent assays with mouse monoclonal antibodies of known specificity, these Fabs reacted with a conformational epitope that includes domains V3 and V4 of the SIV envelope. These neutralizing and nonneutralizing Fabs provide valuable standardized and renewable reagents for studying the role of antibody in preventing or modifying SIV infection in vivo.
Inducible NO synthase expression is low in airway epithelium from young children with cystic fibrosis

Background: This is the first study to measure inducible nitric oxide synthase (iNOS) gene and protein expression quantitatively in primary epithelial cells from very young children with cystic fibrosis (CF). Low levels of exhaled nitric oxide (NO) in CF suggest dysregulation of NO production in the airway. Due to the importance of NO in cell homeostasis and innate immunity, any defect in the pathway associated with CF would be a potential target for treatment. Methods: Cells were obtained by tracheobronchial brushing from 40 children with CF of mean (SD) age 2.1 (1.5) years and from 12 healthy non-atopic children aged 3.4 (1.2) years. Expression of iNOS mRNA was measured using quantitative PCR and iNOS protein by immunofluorescence and Western blot analysis. Results: Inducible NOS mRNA expression was significantly lower in CF patients with and without bacterial infection than in healthy children (0.22 and 0.23 v 0.76; p = 0.002 and p = 0.01, respectively). Low levels of iNOS gene expression were accompanied by low levels of iNOS protein expression as detected by Western blot analysis. Conclusions: These results support the findings of previous studies in adult patients with advanced disease, cell lines, and animal models. Our findings reflect the situation in children with mild lung disease. They indicate that low iNOS expression may be an innate defect in CF with potential consequences for local antimicrobial defence and epithelial cell function and provide evidence for an approach to treatment based on increasing epithelial NO production or the sensitivity of NO dependent cellular processes.
Molecular mechanisms of muscle glucose uptake in response to resistance exercise: a review

Santos JL, Araujo SS, Estevam CS, Lima CA, Carvalho CRO, Lima FB, Marcal AC. Molecular Mechanisms of Muscle Glucose Uptake in Response to Resistance Exercise: A Review. JEPonline 2017;20(4):200-211. Evidence shows that physical exercise carried out systematically promotes numerous health benefits, including improvements in glucose homeostasis. Of all types of physical activity, resistance training is effective in promoting increased strength, speed, power, hypertrophy, and metabolic effects such as increased insulin sensitivity and control in glycogen metabolism. Since there are still gaps requiring attention in regards to the molecular mechanisms leading to effective insulin signaling, this paper attempts to review the effects and implications of resistance exercise on the major intracellular protein activities. In this regard, we set out to understand the role of resistance training on IRS1, IRS2, PI3K, Akt/PKB, and GLUT4 activity, which can lead to the development of possible future interventions to improve physical performance and mitigate the effects of altered metabolic conditions such as obesity, insulin resistance, and type 2 diabetes mellitus.
Feeling like a stranger: negotiations with culture as experienced by Chilean occupational therapists

Abstract Background: Although occupational therapy has begun to focus on the subject of culture, few studies have examined how occupational therapists outside the English-speaking countries reflect on it. Aim: To explore how Chilean occupational therapists reflect on their personal and professional experiences in regard to the complexity of culture, and its different understandings and expressions. Methods: This qualitative study uses content analysis to establish common trends in participants’ experiences. A validation phase and data triangulation were implemented to ensure trustworthiness. Results: Culture is experienced as a continuous negotiation in personal and professional terms. One central theme, ‘negotiating through the dynamism of culture’, and three categories, ‘dealing with power’, ‘understanding local and global identities’, and ‘crossing the boundaries into the client’s land’, emerged. These experiences are complex, chaotic, and highly context-dependent. Discussion: During therapeutic encounters, practitioners and clients may experience cultural barriers even if their differences are not obvious in cultural terms. As a result of this finding, we recommend the inclusion of culture and cultural issues in professional training. The impact of a multicultural research team is discussed. Future research should explore how the construct of culture is introduced in occupational therapy professional training in Chile.
Antipsychotic drug effects on brain morphology in first-episode psychosis.

BACKGROUND Pathomorphologic brain changes occurring as early as first-episode schizophrenia have been extensively described. Longitudinal studies have demonstrated that these changes may be progressive and associated with clinical outcome. This raises the possibility that antipsychotics might alter such pathomorphologic progression in early-stage schizophrenia. OBJECTIVE To test a priori hypotheses that olanzapine-treated patients have less change over time in whole brain gray matter volumes and lateral ventricle volumes than haloperidol-treated patients and that gray matter and lateral ventricle volume changes are associated with changes in psychopathology and neurocognition. DESIGN Longitudinal, randomized, controlled, multisite, double-blind study. Patients treated and followed up for up to 104 weeks. Neurocognitive and magnetic resonance imaging (MRI) assessments performed at weeks 0 (baseline), 12, 24, 52, and 104. Mixed-models analyses with time-dependent covariates evaluated treatment effects on MRI end points and explored relationships between MRI, psychopathologic, and neurocognitive outcomes. SETTING Fourteen academic medical centers (United States, 11; Canada, 1; Netherlands, 1; England, 1). PARTICIPANTS Patients with first-episode psychosis (DSM-IV) and healthy volunteers. INTERVENTIONS Random allocation to a conventional antipsychotic, haloperidol (2-20 mg/d), or an atypical antipsychotic, olanzapine (5-20 mg/d). MAIN OUTCOME MEASURES Brain volume changes assessed by MRI. RESULTS Of 263 randomized patients, 161 had baseline and at least 1 postbaseline MRI evaluation. Haloperidol-treated patients exhibited significant decreases in gray matter volume, whereas olanzapine-treated patients did not. A matched sample of healthy volunteers (n = 58) examined contemporaneously showed no change in gray matter volume. CONCLUSIONS Patients with first-episode psychosis exhibited a significant between-treatment difference in MRI volume changes. Haloperidol was associated with significant reductions in gray matter volume, whereas olanzapine was not. Post hoc analyses suggested that treatment effects on brain volume and psychopathology of schizophrenia may be associated. The differential treatment effects on brain morphology could be due to haloperidol-associated toxicity or greater therapeutic effects of olanzapine.
Gesture Controlled Robot using Image Processing

Service robots directly interact with people, so finding a more natural and easy user interface is of fundamental importance. While earlier works have focused primarily on issues such as manipulation and navigation in the environment, few robotic systems are used with user friendly interfaces that possess the ability to control the robot by natural means. To facilitate a feasible solution to this requirement, we have implemented a system through which the user can give commands to a wireless robot using gestures. Through this method, the user can control or navigate the robot by using gestures of his/her palm, thereby interacting with the robotic system. The command signals are generated from these gestures using image processing. These signals are then passed to the robot to navigate it in the specified directions. In today's age, the robotic industry has been developing many new trends to increase the efficiency, accessibility and accuracy of the systems. Basic tasks could be jobs that are harmful to the human, repetitive jobs that are boring, stressful etc. Though robots can be a replacement to humans, they still need to be controlled by humans itself. Robots can be wired or wireless, both having a controller device. Both have pros and cons associated with them. Beyond controlling the robotic system through physical devices, recent method of gesture control has become very popular. The main purpose of using gestures is that it provides a more natural way of controlling and provides a rich and intuitive form of interaction with the robotic system. This mainly involves Image Processing and Machine Learning for the system or application development. Beyond this, it also requires some kind of hardware for interfacing with the system for gesture control. There are some systems that have been developed in the same field using various techniques. A. Existing Systems
Integrated metabolomic profiling of hepatocellular carcinoma in hepatitis C cirrhosis through GC/MS and UPLC/MS‐MS

The metabolic pathway disturbances associated with hepatocellular carcinoma (HCC) remain unsatisfactorily characterized. Determination of the metabolic alterations associated with the presence of HCC can improve our understanding of the pathophysiology of this cancer and may provide opportunities for improved disease monitoring of patients at risk for HCC development. To characterize the global metabolic alterations associated with HCC arising from hepatitis C (HCV)‐associated cirrhosis using an integrated non‐targeted metabolomics methodology employing both gas chromatography/mass spectrometry (GC/MS) and ultrahigh‐performance liquid chromatography/electrospray ionization tandem mass spectrometry (UPLC/MS‐MS).
Visualizing network data for intrusion detection

As the trend of successful network attacks continue to rise, better forms of intrusion detection and prevention are needed. This paper addresses network traffic visualization techniques that aid an administrator in recognizing attacks in real time. Our approach improves upon current techniques that lack effectiveness due to an overemphasis on flow, nodes, or assumed familiarity with the attack tool, causing either late reaction or missed detection. A port-based overview of network activity produces a improved representation for detecting and responding to malicious activity. We have found that presenting an overview using stacked histograms of aggregate port activity, combined with the ability to drill-down for finer details allows small, yet important details to be noticed and investigated without being obscured by large, usual traffic. Due to the amount of traffic as well as the range of possible port numbers and IP addresses, scaling techniques are necessary to help provide this overview. We provide graphs with examples of forensic findings. Finally, we describe our future plans for using live traffic in addition to our forensic visualization techniques.