Miracle-dz/UniFAR-FTUs huggingface dataset:
Mixed Signals: Regulation of host metabolism by an intracellular bacterial pathogen

Author(s): De Leon, Justin A | Advisor(s): Vance, Russell E | Abstract: A hallmark of all pathogens is an ability to acquire nutrients from hosts. In order to do this, pathogens must overcome both the tight regulation of host nutrients and the host defense mechanisms deployed to protect these nutrients.In the introductory chapter of this dissertation, I begin with a discussion of innate immunity. I discuss the now appreciated view of the innate immune system as a sensor of patterns of pathogenesis. I then argue, based on our studies in Legionella pneumophila, that nutrient acquisition by microbes is a pattern of pathogenesis.In chapter two, I provide experimental evidence that nutrient acquisition is a pattern of pathogenesis. I discuss my work describing how L. pneumophila alters a key metabolic signaling pathway, the mechanistic target of rapamycin complex 1 (mTORC1), in order to free amino acids for nutrition. Using an effector screen, I identified two groups of L. pneumophila Dot-dependent substrates that have opposing consequences on mTORC1. I showed that a family of Legionella glucosyltranferases, Lgt1-3, activate mTORC1 via translation inhibition, resulting in release of host amino acids. These amino acids activate mTORC1 but do so in a counterproductive way: stimulation of mTORC1 leads to the initiation of translation, which consumes the amino acids meant for L. pneumophila. To counter this, L. pneumophila also secretes the SidE family, which inhibits mTORC1 by directly inhibiting the Rag small-GTPases that are required for mTORC1-dependent amino acid sensing. The SidE effectors blind mTORC1 to the amino acids newly freed by the Lgt family. The net result of this battery of SidE and Lgt effectors is to enable L. pneumophila to manipulate the host into liberating amino acids for bacterial consumption.I then close with a perspective chapter that describes the additional questions my work has given rise to and the state of the bacterial molecular pathogenicity field as a whole.
Identification of possible evolutionary pathways of Plum pox virus and predicting amino acid residues of importance to host adaptation

Plum pox virus (PPV) displays significant genetic diversity that has resulted in the identification of several different strains, some that differ in their biological properties and in their geographic distribution. Some strains are limited in their distribution to a single country, while isolates of PPV strain D are found in every country where the virus has been detected. Many questions remain regarding the evolutionary history of PPV: its genetic (strain) diversification, its origin, its dispersal and the distribution of isolates and/or strains. To explore the evolution of PPV, inferred ancestral sequences were reconstructed at various phylogenetic nodes using PAML. Evidence was obtained that indicates that the strains PPV D and PPV M were likely the earliest strains of PPV to evolve. Specifically considered also was the point at which adaptation occurred that allowed infection of Prunus avium and/or Prunus cerasus, sweet cherry and sour cherry, respectively. Eight amino acid sites were identified that appear to have undergone positive selection during this adaptation process. These amino acid sites cluster into two areas, P1 and VPg. These areas of the genome are known to be important for functions such as the control of viral replication rate. In combination with other data, this information sheds light on functionally significant points along the PPV genome and perhaps even characteristics of ancient PPV populations.
Qualitative and Quantitative Videofluoroscopic Analysis of Basic Temporomandibular Movements

Background: The temporomandibular joint (TMJ) is a synovial condylar articulation with freedom of movement resulting from bilateral side morphological interrelations. Its basics movements to attend its main function are rotation and translation. Material and Methods: A videofluoroscopic study of the left posterior oblique incidence comprising 23 healthy volunteers of both sexes was conducted to qualify and quantify the displacement of the mandible over the temporal surface. This evaluation was performed without using any artificial contrast medium. Results: From maximum occlusion to maximum mouth opening, three spaces defined as LL1, LL2 and LL3 were established and used to qualify and quantify the limits of mouth opening. Seventeen volunteers could be classified as normal free (NF) and six as suspicious (S) based on this function. Conclusion: The NF and S groups statistically differed in their mouth opening capabilities (p < 0.0001). Measured values for LL3 greater than LL2 as well as positive values for L3-L2 can be considered NF and negative values for L3-L2 can be considered S with a significance of p < 0.0001. L2 was statistically confirmed as a good parameter for the distinction between normal and suspicious TMJ functioning. Keywords— temperomandibular joint, pterygoid muscles, temporal bone.
Potensi makanan fermentasi khas Indonesia sebagai imunomodulator

Indonesia merupakan negara kepulauan dengan berbagai suku dan budaya. Perbedaan budaya menyebabkan berbeda jenis makanan khas yang ada di Indonesia. Makanan hasil pengolahan dengan fermentasi dapat dijumpai hampir di setiap daerah. Pengolahan makanan dengan bioteknologi konvensional yang berupa fermentasi melibatkan berbagai mikroorganisme. Senyawa hasil metabolisme mikroba yang hidup pada bahan baku pangan merupakan prebiotik yang memiliki manfaat bagi kesehatan. Begitu pula mikroba yang hidup pada makanan terfermentasi yang masuk ke dalam tubuh, disebut sebagai probiotik, mampu meningkatkan fungsi imun. Sehingga makanan terfermentasi memiliki potensi sebagai pengatur sistem imun (imunomodulator) di dalam tubuh manusia. Artikel ini mengulas potensi bahan makanan dengan pengolahan fermentasi yang berasal dari berbagai daerah di Indonesia sebagai agen imunomodulator.
Broad-scale coastal movements of white sharks off Western Australia described by passive acoustic telemetry data

Movements of 89 acoustically tagged subadult and adult white sharks (Carcharodon carcharias) were monitored off the south and west coasts of Western Australia (WA) between December 2008 and May 2016 by a network of up to 343 passive acoustic receivers. In all, 290 inter-regional movements, totalling 185092km were recorded for 73 of these sharks. Estimated rates of movement in excess of 3kmh–1 (mean 1.7kmh–1; maximum 5.6kmh–1) were common, even over distances of thousands of kilometres. Detections indicated that white sharks may be present off most of the south and lower west coasts of WA throughout the year, although they are more likely to be encountered during spring and early summer and are least likely to be present during late summer and autumn. There was limited evidence of predictable return behaviour, seasonal movement patterns or coordination of the direction and timing of individual shark’s movements. Nevertheless, the data suggest that further analyses of movements in relation to ecological factors may be useful predictors of shark activity at local scales. It is hoped that these data may be useful for informing public safety initiatives aimed at mitigating the risks associated with human encounters with white sharks off the WA coast.
Place du méthotrexate à faible dose en prévention des événements athérosclérotiques : étude CIRT

Stéphanie Blais-Lapointe1-3, Pharm.D. , M.Sc., Mary Ghattas1,4,5, B.Pharm. , M.Sc. Audrey Larouche1-3, Pharm.D. , M.Sc., Justine Pagé1,4,6, Pharm.D. , M.Sc. 1Candidate à la maîtrise en pharmacothérapie avancée au moment de la rédaction, Faculté de pharmacie, Université Laval, Québec (Québec) Canada; 2Résidente en pharmacie au moment de la rédaction, Centre intégré universitaire de santé et de services sociaux de la Mauricie-et-du-Centre-du-Québec – Centre hospitalier affilié universitaire régional, Trois-Rivières (Québec) Canada; 3Pharmacienne, Centre intégré universitaire de santé et de services sociaux de la Mauricie-et-du-Centre-du-Québec – Centre hospitalier affilié universitaire régional, Trois-Rivières (Québec) Canada; 4Résidente en pharmacie au moment de la rédaction, Institut universitaire de cardiologie et de pneumologie de Québec – Université Laval, Québec (Québec) Canada; 5Pharmacienne, Adjointe au chef du département de pharmacie, Centre intégré universitaire de santé et de services sociaux de la Montérégie-Ouest – Hôpital du Suroît, Salaberry-de-Valleyfield (Québec) Canada; 6Pharmacienne, Centre intégré de santé et de services sociaux de Chaudière-Appalaches, site Hôtel-Dieu de Lévis, Lévis (Québec) Canada
Improving dynamic programming for travelling salesman with precedence constraints: parallel Morin–Marsten bounding

The precedence constrained traveling salesman (TSP-PC), also known as sequential ordering problem (SOP), consists of finding an optimal tour that satisfies the namesake constraints. Mixed integer-linear programming works well with the ‘lightly constrained’ TSP-PCs, close to asymmetric TSP, as well as the with the ‘heavily constrained’ (Gouveia, Ruthmair, 2015). Dynamic programming (DP) works well with the heavily constrained (Salii, 2019). However, judging by the open TSPLIB SOP instances, the worst for any method are the ‘medium’. We implement a parallel Morin–Marsten branch-and-bound scheme for DP (DPBB). We show how the lower bound heuristic parameterizes DPBB's worst-case complexity and DPBB ‘inherits’ the abstract travel cost aggregation feature of the DP, permitting its direct use with both the conventional and bottleneck TSP-PC. The scheme was tested on TSPLIB instances, with best known upper bounds (TSP-PC), or those found by restricted DP (Bottleneck TSP-PC), and lower bounds from a greedy-type heuristic. Our OPENMP-based parallel implementation achieved 20-fold speedup for larger instances. We close the long-standing kro124p.4. sop (conventional TSP-PC) and both kro124p.4. sop and ry48p.2. sop (Bottleneck TSP-PC).
Skeletal muscle status, autonomic balance and short-term results of cardiac surgery

Type of funding sources: Public hospital(s). Main funding source(s): Research Institute for Complex Issues of Cardiovascular Diseases The aim - investigate the association of the lower extremities skeletal muscle state, status autonomic nervous system (ANS) and short-term results of the cardiac operations. Design Study included 64 patients, who underwent planned cardiac surgery. All subjects before surgery performed a routine laboratory and instrumental examinations, six-minute walk test (6MWT), and static-dynamic tests on the training device. ANS was carried out, using ORTOexpert software. Were formed 2 groups – with the combined endpoint CEP (n = 9) and without CEP (n = 55). CEP included: perioperative development stroke, myocardial infarction, persistent arrhythmias and heart block, multiple organ dysfunction syndrome, death. Results Not found difference between the groups in gender, age, in main clinical data and laboratory tests indicators, and in endurance of the skeletal muscles or the 6MWT. In the CEP group, strength of skeletal muscles of the upper and lower extremities was lower, initially more pronounced sympathetic activation and larger values of the power of the frequency spectrum (TF). Stress index (IS) was lower in the CEP group, but after transitioning orthostatic position it surpassed the number without CEP. One-factor logistic regression analysis established factors associated with the development of CEP - poor muscle status, peripheral atherosclerosis; high EuroSCORE, cardiopulmonary bypass duration (CBD) and ANS disbalance. Multivariate regression analysis to establish the relationship of poor skeletal muscle status, pronounced sympathicotonia and a high incidence of postoperative complications. Logistic regression analisys Odds ratio [ -95%; +95%CL] p One-factor logistic regression Stenosis ICA ≥ 30% 9,545 [1,030; 88,467] ,043 Shoulder Girdle Muscle Strength (Kg) 0,893 [0,786; 1,001] ,048 Knee extensors strength (kg) 1,012 [0,997; 1,029] ,098 Amo (basic) 0,958 [0,920; 0,998] ,037 IS (basic) 0,996 [0,990; 1,000] ,096 EuroSCORE (points) 1,643 [1,003; 2,694] ,043 CBD (min) 1,010 [1,001; 1,022] ,068 Multiple-factor logistic regression p=,001 LF/HF 1,175 [0,972; 1,420] ,088 Amo (basic) 0,950 [0,905; 0,997] ,034 Shoulder Girdle Muscle Strength (Kg) 0,863 [0,750; 0,993] ,036 LF/HF-ratio Low frecuency/High frecuency Amo-mode amplitude
Abundance, occurrence, and seasonality of the Subtropical Doradito (Pseudocolopteryx acutipennis) on the coast of Brazil

ABSTRACT The Subtropical Doradito (Pseudocolopteryx acutipennis) is a small tyrannid that breeds in shrubby marshlands of South America. Post-breeding migration occurs in both mountain and lowland populations, but little is known of the destination(s) of these birds. Subtropical Doraditos have recently been found during the southern winter, or non-breeding season, in several localities in southern Amazonian Brazil and the Pantanal, with four reports from coastal Brazil. Our observations and censuses in coastal marshes of southeast and southern Brazil have produced eight records of Subtropical Doradito in the states of Paraná and São Paulo. In light of comparison with other Brazilian records compiled for this study, we suggest that coastal winterers are likely latitudinal migrants from geographically restricted breeding grounds in the Pampas of Argentina. In addition, we discuss conservation problems for the Subtropical Doradito in coastal wintering areas.
Melatonin: A Powerful Integrative Adjunctive Agent for Oncology

Melatonin is an established hormone supplement and has been well recognized for its effect on the circadian cycle to improve sleep, REM (rapid eye movement), and aiding in jetlag recovery. The utility of melatonin extends beyond sleep aid, however. This hormone also possesses less well-known antioxidant action and even robust anticancer activity. Melatonin may be a key supplement for addressing age-related neurologic decline while serving as a valuable adjunctive cancer treatment that reduces drug resistance in tumors and downregulates angiogenesis. In immunotherapy, melatonin activates Natural Killer (NK) cells nested within tumoral tissue and does not have the side effect profile of other immunoreactive agents used for chemotherapy. Since melatonin is found in high concentrations in the brain and other hormone-linked tissues, the relevance of melatonin is increased for the treatment of estrogen-linked cancers. The immunomodulatory effect of melatonin may also help with chronic inflammation seen in patients with autoimmune disorders. All of these effects together represent a unique and versatile therapeutic agent for integrative medicine. No other commercially available drug possesses all of these therapeutic mechanisms while having a very minimal side effect profile and being considered overall to be safe to use. Currently, melatonin is underutilized in medicine, especially in the field of integrative oncology and represents a crucial supportive adjuvant to improve the lives of patients.
Isoflavones as constituents of plant foods : Isoflavone als Bestandteile pflanzlicher Lebensmittel

Vor dem Hintergrund der Diskussion uber die ernahrungsphysiologische Bedeutung von Isoflavonen befasst sich die vorliegende Ubersichtsarbeit auf der Basis von 186 Literaturquellen mit der Struktur, dem Vorkommen, der Aufnahme, der Biosynthese, der Resorption, dem Metabolismus und der biologischen Wirkung dieser Untergruppen der Pflanzenphenole. Diskutiert werden sowohl positive als auch negative biologische Wirkungen dieser Verbindungen. Strukturabhangig konnen die Isoflavone mit anderen Lebensmittelinhaltsstoffen in Wechselwirkung treten. With the background of the actual ongoing discussion on the nutritional
Engaging Students in Curriculum Development Through Design Thinking: A Course Design Case

This design case documents the motivations, decisions, and results of an experimental course that involved students in the curriculum development process through the use of design thinking methodology. Primary points of student input were determining assignment topics, developing learning objectives, and contributing to the design of grading assessment. The case also examines the student experience and provides a detailed evaluation of the process, including an assessment of the benefits of the approach and a dissection of the unforeseen obstacles in the design process. In this investigation into the intention and execution of the course, educators may find the inspiration and framework to adapt this approach for their own courses.
Factors Influencing Survival Rates of Pronghorn Fawns in Idaho

Pronghorn (Antilocapra americana) occur throughout western North America. In Idaho, USA, following intensive hunting to reduce crop depredations in the late 1980s, pronghorn populations have not rebounded to desired levels. Because neonatal survival in ungulates is one factor limiting population growth, we evaluated cause‐specific mortality and the influence of intrinsic and extrinsic factors on survival rates of 217 radio‐collared pronghorn fawns across 3 study areas in Idaho during 2015–2016. For intrinsic variables, we determined the sex and body mass index (BMI) for each fawn. For extrinsic variables, we determined the abundance of predators and alternate prey, estimated the normalized difference vegetation index (NDVI) for 1 month pre‐ and post‐parturition, and measured fecal nitrogen and diaminopimelic acid (DAPA). We considered NDVI as a measure of plant productivity, and fecal nitrogen and DAPA as possible proxies of diet quality. We predicted NDVI, fecal nitrogen, and DAPA would be positively related to the nutritional status of females and positively related to fawn survival. We used Program MARK with known fate models to estimate semi‐monthly survival rates of pronghorn fawns for the first 4 months post‐parturition. During both years, the leading cause of fawn mortality was coyote (Canis latrans) predation (58%), followed by unknown causes of mortality (18%), unknown predation (12%), predation by bobcats (Lynx rufus; 6%), predation by golden eagles (Aquila chrysaetos; 3%), and other (3%). Mean fawn survival for the 4 months post‐parturition across years and study sites was 0.42± 0.04 (SE; range= 28–62%). The top survival model included BMI, lagomorph abundance, and DAPA and had a model weight of 83.3%. All 3 variables were positively related to pronghorn fawn survival. Because females with increased nutrition generally have heavier fawns, BMI was likely correlated to diet quality, which was supported by the positive relationship between DAPA and fawn survival. We hypothesize that high lagomorph abundance created an alternate prey base to buffer coyotes from preying on pronghorn neonates. We found no influence of measures of NDVI (pre‐ and post‐parturition), fecal nitrogen, or predator abundance on fawn survival. Management actions providing high‐quality forage for pronghorn are likely to contribute to production of heavier fawns having the highest chance of survival. © 2020 The Wildlife Society.
Constituency and coincidence in Chácobo (Pano)

Abstract This paper provides a detailed description of the results of 24 constituency diagnostics, both morphosyntactic and phonological, to Chacobo, a southern Pano language of the northern Bolivian Amazon. While it is often assumed that misalignments across the domains that emerge from constituency diagnostics can be resolved by reference to a distinction between phonological and morphosyntactic words, I argue that this is not true of Chacobo. Divergence is at least as high within phonological domains and morphosyntactic domains as it is across them. While it is often assumed that domains tend to converge overall on a single wordhood candidate or that domain divergence is marginal, I argue that this is not true of Chacobo. I present a cluster of methodologies that assess the motivation for a word constituent as an empirical hypothesis, rather than treating it as an a priori assumption. No strong evidence for a word constituent emerges from the Chacobo data. Theoretical and methodological implications are discussed.
Bacterial Elicitation of Transcriptional Response of Female Squash Bug, Anasa tristis (De Geer)1

Abstract. The squash bug, Anasa tristis (De Geer), is a major pest of squash, pumpkin, and other cucurbits throughout North America. A. tristis is a piercingsucking feeder that causes extensive foliar wilting and fruit scarring and transmits plant pathogens. Current biological agents to control A. tristis are limited in efficacy, and newer control methods must be developed. Here we present studies of immune system transcripts as the initial step in identifying potentially vulnerable targets for control of gene expression. Following immune stimulation with bacteria, transcript levels of six components of the inducible innate system in adult female A. tristis were measured using quantitative PCR. An antibacterial peptide-encoding transcript, anacin; an enzyme central to melanization, prophenoloxidase; and three sentinel proteins, scavenger receptor, β-1,3-glucan-binding protein, and peptidoglycan-binding protein were upregulated by bacterial elicitation. Expression of a putative immunoregulatory cytokine, astakine, was identified and increased by septic puncture. We also found novel upregulation of an enzyme of central energy metabolism, arginine kinase, in response to septic puncture of A. tristis adults.
Predicting Homophily and Social Network Connectivity From Dyadic Behavioral Similarity Trajectory Clusters

The similarity between pairs of people is often measured on relatively static traits and at a given point in time. Moving beyond this approach, a burgeoning line of research is investigating temporal dyadic similarity on traits and behaviors, such as health activities. Our study contributes to this line of inquiry by using fine-grained longitudinal data obtained from sensors, mobile devices, and surveys to examine whether we can observe distinct types of dyadic similarity trajectories based on physical activity, and if so, what dyad-level properties predict membership in each trajectory class. Treating daily differences in the steps for dyads as time series, we use k-shape clustering to identify classes of similarity trajectories and logistic regression to examine the link between trajectory class and key dyad-level factors. We identify 21 dyadic trajectory clusters and find that trajectory membership predicts dyadic connectivity in the communication network, as well as racial and religious—but not gender-based—similarity. We conclude by noting how research on dyadic similarity trajectories can be further integrated with ongoing work in social network analysis.
Experimental Evidence of a Twofold Electromagnetic Enhancement Mechanism of Surface-Enhanced Raman Scattering

The surface-enhanced Raman scattering (SERS) electromagnetic (EM) enhancement mechanism is a two-fold enhancement process in which both the incident and scattered Raman fields are enhanced. In this letter, we present new direct evidence of the two-fold EM mechanism by using an Ag nanorod array/SiO2 dielectric layer/Ag mirror multilayer thin film "local plasmon resonator". The two-fold EM enhancement mechanism of SERS was confirmed by analyzing the optical absorption and Raman scattering spectra of the local plasmon resonator for excitation and scattered light. The effect of light interference was altered by varying the film thickness of the SiO2 phase control layer (PCL), and the absorbance in the Raman scattering wavelength range was reduced from 90% to 0%. We also demonstrated that the intensity of the background emission is closely related to the enhancement of the scattered field and provides substantial evidence for a two-fold SERS enhancement mechanism.