Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection

Intracellular colonization and persistent infection by the kinetoplastid protozoan parasite, Trypanosoma cruzi, underlie the pathogenesis of human Chagas disease. To obtain global insights into the T. cruzi infective process, transcriptome dynamics were simultaneously captured in the parasite and host cells in an infection time course of human fibroblasts. Extensive remodeling of the T. cruzi transcriptome was observed during the early establishment of intracellular infection, coincident with a major developmental transition in the parasite. Contrasting this early response, few additional changes in steady state mRNA levels were detected once mature T. cruzi amastigotes were formed. Our findings suggest that transcriptome remodeling is required to establish a modified template to guide developmental transitions in the parasite, whereas homeostatic functions are regulated independently of transcriptomic changes, similar to that reported in related trypanosomatids. Despite complex mechanisms for regulation of phenotypic expression in T. cruzi, transcriptomic signatures derived from distinct developmental stages mirror known or projected characteristics of T. cruzi biology. Focusing on energy metabolism, we were able to validate predictions forecast in the mRNA expression profiles. We demonstrate measurable differences in the bioenergetic properties of the different mammalian-infective stages of T. cruzi and present additional findings that underscore the importance of mitochondrial electron transport in T. cruzi amastigote growth and survival. Consequences of T. cruzi colonization for the host include dynamic expression of immune response genes and cell cycle regulators with upregulation of host cholesterol and lipid synthesis pathways, which may serve to fuel intracellular T. cruzi growth. Thus, in addition to the biological inferences gained from gene ontology and functional enrichment analysis of differentially expressed genes in parasite and host, our comprehensive, high resolution transcriptomic dataset provides a substantially more detailed interpretation of T. cruzi infection biology and offers a basis for future drug and vaccine discovery efforts.
Iterative combinatorial auctions: achieving economic and computational efficiency

ITERATIVE COMBINATORIAL AUCTIONS: ACHIEVING ECONOMIC AND COMPUTATIONAL EFFICIENCY David Christopher Parkes Supervisor: Lyle H. Ungar This thesis presents new auction-based mechanisms to coordinate systems of selfinterested and autonomous agents, and new methods to design such mechanisms and prove their optimality. Computation is increasingly carried out on open networks, with self-interested programs (\agents"), competing to derive the most utility for users. In addition, new interconnectivity and distributed computing is changing business practices. It is now possible to implement dynamic mechanisms to trade goods and services, both business-to-consumer (B2C) and business-to-business (B2B), and remove the ine ciencies in traditional marketplaces. Auctions o er great promise as simple and robust dynamic mechanisms for e cient resource allocation. There are already on-line consumer auctions, and nascent auctions for B2B trade in the supply-chain. However the majority of on-line auctions remain simple variations on standard auctions. My thesis is that it is necessary to take an explicitly computational approach to auction design. Auctions will be populated with automated bidding agents, and only auctions that are robust and present simple optimal bidding strategies will be successful. In addition, combinatorial auctions are important in many important applications, but present inherently hard computational problems for agents and for auctioneers. A combinatorial auction allows agents to bid for bundles of items. Consider a manufacturer that needs either components A and B, or just component C; consider a mobile agent that needs an interval of compute time; consider a train that needs a bundle of
Emerging approaches in Parkinson’s disease – adjunctive role of safinamide

Ongoing neuronal death in Parkinson’s disease (PD) causes an altered neurotransmission of various biogenic amines, particularly dopamine. As these changes do not follow a distinct pattern, they vary individually, and are differently pronounced. As a result, a heterogeneous onset of motor and nonmotor features occurs in each patient with PD during the whole course of the disease. PD actually describes a set of distinct diseases that manifest themselves in clinical syndromes with certain similarities but also great differences. This clinical picture responds to drugs with a broad spectrum of modes of actions better than to compounds with an exclusive focus on specific receptor subtypes. Therefore, safinamide is an ideal candidate for treatment of patients with PD, since its pharmacological profile includes reversible monoamine oxidase-B inhibition, blockade of voltage-dependent sodium channels, modulation of calcium channels, and inhibition of glutamate release. Safinamide is applied only once daily. Its oral dose ranges from 50 to 100 mg. Safinamide was well tolerated and safe in the clinical development program that demonstrated the amelioration of motor symptoms and OFF phenomena by safinamide when combined with dopamine agonists or levodopa. In the real world of maintenance of patients with PD, effects of safinamide application resemble therapy with classical monoamine oxidase inhibitors or amantadine in combination with other dopamine-substituting drugs. Safinamide is becoming increasingly available in the EU despite complex approval and pricing scenarios.
Skeletal Malocclusion: A Developmental Disorder With a Life-Long Morbidity

The likelihood of birth defects in orofacial tissues is high due to the structural and developmental complexity of the face and the susceptibility to intrinsic and extrinsic perturbations. Skeletal malocclusion is caused by the distortion of the proper mandibular and/or maxillary growth during fetal development. Patients with skeletal malocclusion may suffer from dental deformities, bruxism, teeth crowding, trismus, mastication difficulties, breathing obstruction and digestion disturbance if the problem is left untreated. In this review, we focused on skeletal malocclusion that affects 27.9% of the US population with different severity levels. We summarized the prevalence of class I, II and III of malocclusion in different ethnic groups and discussed the most frequent medical disorders associated with skeletal malocclusion. Dental anomalies that lead to malocclusion such as tooth agenesis, crowding, missing teeth and abnormal tooth size are not addressed in this review. We propose a modified version of malocclusion classification for research purposes to exhibit a clear distinction between skeletal vs. dental malocclusion in comparison to Angle’s classification. In addition, we performed a cross-sectional analysis on orthodontic (malocclusion) data through the BigMouth Dental Data Repository to calculate potential association between malocclusion with other medical conditions. In conclusion, this review emphasizes the need to identify genetic and environmental factors that cause or contribute risk to skeletal malocclusion and the possible association with other medical conditions to improve assessment, prognosis and therapeutic approaches.
Immune System and Bone Regeneration

Kenneth A. Johnson bone, resulting in delayed or non-union is a vexing clinical problem in all species of animals. Recently, the focus of attention in orthopaedics has been on the treatment of fractures by bone grafts, mesenchymal stem cells, growth factors, biomaterials and improved mechanical environment, either alone or in some combination. These therapies have produced clearly demonstrable benefits in treating delayed and non-union. However there is still much to learn about the complex processes of fracture healing, and why it fails in some patients despite the management by ‘state of the art’ surgery employing, for example, minimally invasive osteosynthesis, locking implants, exogenous growth factor application, and 3D printed biomaterials and stem cells for the reconstruction of critical sized defects. Even so, in a proportion of fracture patients, endogenous factors predispose to impaired fracture healing. The pivotal role of immunity in fracture healing and bone regeneration was one such endogenous factor under discussion at the symposium. The immune system has direct involvement in guiding all stages of fracture healing starting with inflamImmune System and Bone Regeneration
Relationship between vitamin and calcium supplement use and colon cancer.

The relationship between vitamin supplement use and colon cancer was assessed in a population-based case-control study among men and women aged 30-62 years. Cases were 251 men and 193 women diagnosed with colon cancer in 1985-1989 in three counties in the Seattle metropolitan area who were identified from the Surveillance, Epidemiology, and End Results cancer registry. Controls were 233 men and 194 women identified by random digit dialing. Supplement use was assessed by questions on frequency, duration, and dose per day (for individual supplements) or type (for multivitamins) during the 10-year period ending 2 years before diagnosis. All results were adjusted for age and sex and were not confounded by other measured behaviors. The average daily intake of supplemental vitamins A, C, E, folic acid, calcium, and multivitamins during the reference period were each associated with reduced risk of colon cancer (all P for trend < 0.03). The strongest associations were for use of vitamin E (odds ratio, 0.43; 95% confidence interval, 0.26-0.71 for > or = 200 IU/day versus none) and multivitamins (odds ratio, 0.49; 95% confidence interval, 0.35-0.69 for daily use versus no use; both P for trend < 0.001). These two associations were also significant using a stricter test of trend limited to supplement users, which reduces the effect of colinearity among these exposures. Because almost all vitamin D supplementation comes from multivitamin pills, the association of vitamin D use with colon cancer could not be distinguished from that of multivitamin use. Clinical trials or cohort studies with long-term assessment would be needed before public health recommendations could be made about supplement use.
A Composite Descriptor for Shape Retrieval

In this paper, a composite descriptor for shape retrieval has been proposed. The proposed descriptor is obtained from generic fourier descriptors (GFD) for the shape region and the shape contour. A composite descriptor derived from GFD of the shape region and the shape contour is used for indexing and retrieval of shapes. Difference between two images is computed as the Euclidean distance between their composite descriptors. Experiments are performed to test the effectiveness of the proposed descriptor for retrieval of 2d images. Sets of composite descriptors, obtained by assigning different weights to the region component and the contour component, are also evaluated. Item S8 within the MPEG-7 still images content set is used for performing experiments; this dataset consists of 3621 still images. Experimental results show that the proposed descriptor is effective.
Complaining Behaviors in Restaurants New Roles in Failure Scenarios

Abstract Customers’ complaining behavior has become a key issue in the restaurant industry. The present study investigated the effects of customer involvement, service stages and failure severity as manipulating factors on customers’ complaining behavior in fine dining restaurants. Based on a 2×4×2 between subjects experiment, data were collected from a sample of 714 randomly selected Iranian customers of 4 well known fine dining restaurants of Tehran. Public actions, negative marketing actions, and asking for recovery actions were extracted by an exploratory factor analysis as the three main components of complaint behavior. Also, a discriminant analysis was performed to determine the underlined construct of components, and 3-way factorial ANOVAs and MANOVA tests were administered to examine the effects and interactions. Most of the effects were meaningful especially in case of service stages and failure severity. Findings showed that different interactions of factors resulted in different components of complaint behavior. Due to the nature of these components, their consequent damages were significant and hidden for managers/owners in some cases. In other cases, customers provide an opportunity of recovery for restaurants. In general, study findings have major contributions to the better understanding of different service failures and help both researchers and restaurant managers to deal with them effectively. Also, precious suggestions in the conclusion section are useful for avoiding failures, especially serious ones, in food establishments.
Scientists and Engineers Study Chaucer and Wordsworth: Peer Perspectives on the Teaching of Poetry.

A kind of culture shock awaits new humanities teachers. Surrounded in their student years by peers and faculty who share their humanistic values and interests in the beauty, complexity, and ambiguity of written language, college English instructors typically find themselves teaching many students who take their courses not because they love literature, as their teachers do, but because they are required to. Drawn largely (but not exclusively) from science and technology, such students are not committed to literature and are sometimes suspicious of the entire enterprise. How might teachers overcome the distance between their students and themselves? To explore this question and to find out, as Tobias phrases it, what makes the humanities "off-putting", we invited fourteen Cornell University professors of science and technology to situate themselves as learners in a week-long mini-course on poetry. While they read, listened, and wrote papers, they recorded their reactions to the material and to the process. The experiment was modeled on a series of "Peer Perspectives on Science" workshops in which professors from disciplines other than science stand in as surrogate learners in artificially constructed "classes" in science. Tobias had invented the technique in order to get at what makes science (and mathematics) "hard" for students in the humanities and social science. Her choice of the term "peers" was meant to convey the similarity of student and instructor, alike in intelligence, motivation, and experience in learning; different only in their newness to one another's fields (Blakeslee, 1986; Tobias, 1985, 1986, 1988; Tobias & Hake, 1988). From "Peer Perspectives on Science," had come valuable feedback for instructors of science. The experiment at Cornell, we hoped, would help us understand the problems and possibilities of teaching literature to science students. Fourteen scientists and engineers, then chemists, materials scientists, geologists, applied mathematicians, and physicists agreed to read
The Impact of Vitamin D on Dendritic Cell Function in Patients with Systemic Lupus Erythematosus

Background Excessive activity of dendritic cells (DCs) is postulated as a central disease mechanism in Systemic Lupus Erythematosus (SLE). Vitamin D is known to reduce responsiveness of healthy donor DCs to the stimulatory effects of Type I IFN. As vitamin D deficiency is reportedly common in SLE, we hypothesized that vitamin D might play a regulatory role in the IFNα amplification loop in SLE. Our goals were to investigate the relationship between vitamin D levels and disease activity in SLE patients and to investigate the effects of vitamin D on DC activation and expression of IFNα-regulated genes in vitro. Methodology/Principal Findings In this study, 25-OH vitamin D (25-D) levels were measured in 198 consecutively recruited SLE patients. Respectively, 29.3% and 11.8% of African American and Hispanic SLE patient had 25-D levels <10 ng/ml. The degree of vitamin D deficiency correlated inversely with disease activity; R = −. 234, p = . 002. In 19 SLE patients stratified by 25-D levels, there were no differences between circulating DC number and phenotype. Monocyte-derived DCs (MDDCs) of SLE patients were normally responsive to the regulatory effects of vitamin D in vitro as evidenced by decreased activation in response to LPS stimulation in the presence of 1,25-D. Additionally, vitamin D conditioning reduced expression of IFNα-regulated genes by healthy donor and SLE MDDCs in response to factors in activating SLE plasma. Conclusions/Significance We report on severe 25-D deficiency in a substantial percentage of SLE patients tested and demonstrate an inverse correlation with disease activity. Our results suggest that vitamin D supplementation will contribute to restoring immune homeostasis in SLE patients through its inhibitory effects on DC maturation and activation. We are encouraged to support the importance of adequate vitamin D supplementation and the need for a clinical trial to assess whether vitamin D supplementation affects IFNα activity in vivo and, most importantly, improves clinical outcome.
A stateless mechanism for providing Quality of Service in the Internet

We investigate the problem of providing a fair bandwidth all ocation to each of n flows that share the outgoing link of a congested router. The buffer at the outgoing link is a simple FIFO, shared by packets belonging to the n flows. We devise a simple packet dropping scheme, called CHOKe, that discriminates a gainst the flows which submit more packets/sec than is allowe d by their fair share. By doing this, the scheme aims to approxima te the fair queueing policy. Since it is stateless and easy to implement, CHOKe controls unresponsive or misbehaving flows with a mini um overhead.
Examining the Engagement of Transfer Students in Texas Universities

The success of transfer students plays a critical role in improving the baccalaureate attainment rates of undergraduates attending 4-year higher education institutions in Texas; however, current indicators suggest transfer students have lower persistence and graduation rates relative to students who begin and complete their college education at one university (i.e., non-transfer students). Additionally, the research literature indicates a link between degree completion and engagement; however, transfer students are reported to be less engaged and less likely to persist than their counterparts. This quantitative study compared the engagement experiences of 2-year transfers, 4-year transfers, swirl transfer, and non-transfers by using National Survey of Student Engagement (NSSE) 2008 data to determine if there are any differences among these groups, and if these differences persist after controlling for individual and institutional covariates. the sample consisted of 2,000 seniors attending 4-year higher education institutions in Texas. the engagement scores of each group were compared using a multivariate analysis (MANOVA). This study found non-transfers were more engaged than each type of transfer student on Student-Faculty Interaction and Supportive Campus Environment factors; moreover, these differences generally persisted after controlling for residence, enrollment status, and institutional control (i.e., public vs. private). The data indicated no difference among the three transfer sub-groups for any of the engagement variables, which suggests their engagement experiences were similar. This research suggests that efforts to increase the participation and success rates of Texans, particularly those described as transfers, may be informed by how students perceive their engagement experiences; consequently, institutions may consider modifying and implementing policies that promote student participation in educationally purposeful activities leading to persistence and graduation.
On accident analysis and slip-resistance measurement.

Four accident analysis models are discussed in relation to a specimen slipping accident. One classification, or ‘single-type’ model, commonly used in accident statistics, lumps all events and agencies from each accident in one ‘cause’ group. This may lead to serious underestimates of particular hazards. In past occupational injury statistics for Sweden, slipping appeared in less than 5 % of all accidents during 1975. With an entirely different sequential model of the present statistics system (‘ISA’, recording about 100 descriptors for each of more than 100000 annual accidents), slipping has been registered in more than 77% of all accidents during 1979. Fault-trees and dynamic work analysis models are considered for case studies and hazard descriptions. Having identified a major hazard, appropriate techniques and criteria must be developed for safety performance tests. Reports of more than 60 different slip-resistance meters have been found in the literature. Many of the meters are designed to gauge the s.
FGF6 regulates muscle differentiation through a calcineurin‐dependent pathway in regenerating soleus of adult mice

Important functions in myogenesis have been proposed for FGF6, a member of the fibroblast growth factor family accumulating almost exclusively in the myogenic lineage, but its precise role in vivo remains mostly unclear. Here, using FGF6 (−/−) mice and rescue experiments by injection of recombinant FGF6, we dissected the functional role of FGF6 during in vivo myogenesis. We found that the appearance of myotubes was accelerated during regeneration of the soleus of FGF6 (−/−) mice versus wild type mice. This accelerated differentiation was correlated with increased expression of differentiation markers such as CdkIs and calcineurin, as well as structural markers such as MHCI and slow TnI. We showed that an elevated transcript level for calcineurin Aα subunit correlated with a positive regulation of calcineurin A activity in regenerating soleus of the FGF6 (−/−) mice. Cyclin D1 and calcineurin were up‐ and down‐regulated, respectively in a dose‐dependent manner upon injection of rhFGF6 in regenerating soleus of the mutant mice. We showed an increase of the number of slow oxidative (type I) myofibers, whereas fast oxidative (type IIa) myofibers were decreased in number in regenerating soleus of FGF6 (−/−) mice versus that of wild type mice. In adult soleus, the number of type I myofibers was also higher in FGF6 (−/−) mice than in wild type mice. Taken together these results evidenced a specific phenotype for soleus of the FGF6 (−/−) mice and led us to propose a model accounting for a specific dose‐dependent effect of FGF6 in muscle regeneration. At high doses, FGF6 stimulates the proliferation of the myogenic stem cells, whereas at lower doses it regulates both muscle differentiation and muscle phenotype via a calcineurin‐signaling pathway. © 2005 Wiley‐Liss, Inc.
MPC of Switching in a Boost Converter Using a Hybrid State Model With a Sliding Mode Observer

In this paper, a model of a DC-DC (boost) converter is first expressed as a hybrid/switched/variable-structure system state model for the purpose of applying recently developed hybrid optimal control theory to control switching in a boost converter. Switching control is achieved by forming the embedded form of the hybrid state model, which enables the derivation of a control that solves for the switching function that minimizes a user-defined performance index. This approach eliminates the need to form average-value models and provides flexibility to balance competing objectives through appropriate weighting of individual terms in the performance index. Since, in practical situations, both the source voltage and the load resistance vary with time in unknown and unmeasurable ways, we introduce a sliding mode observer based on an enlarged state model which allows implicit estimation of the unknown variables. The combined optimal switching control and sliding mode observer are applied to a boost converter in which several nonidealities and losses are represented. The results of time-domain simulation and hardware experiments are used to validate and compare the response of the hybrid optimal control-sliding mode observer to that of a traditional current-mode control strategy.