Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal Study of the Prevalence and Prognostic Implications of Oral Manifestations in Romanian Children Infected with Human Immunodeficiency Virus Type 1

Objective: We evaluated the prevalence and predictive value for human immunodeficiency virus (HIV) disease progression of oral manifestations in Romanian children. Methods: A nonrandom sample of 238 HIV-infected children was followed prospectively between 1998 and 2001 at the Romanian-American Children's Center in Constanta, Romania. Study subjects underwent comprehensive annual oral examinations. Oral manifestations of interest, demographic data and other selected medical information were recorded at baseline and at each subsequent visit. Descriptive statistics and survival analysis methods were used in the study. A level of statistical significance of α = 0.05 was used. Results: The study subjects' mean age was 9.9 ± 1.2 (SD) years. The most common oral lesions were gingivitis (49%), parotid enlargement (13%) and oral candidiasis (11%). Oral candidiasis was associated with progression to acquired immunodeficiency syndrome or death (whichever occurred first) (log rank P = 0.03) and with death (log rank P < 0.001). Oral hairy leukoplakia also was associated with progression to death (log rank P = 0.001). The risk of dying was 3.43 (95% confidence interval, 1.86–6.34; P < 0.001) for children who had oral candidiasis at baseline and 4.62 (95% confidence interval, 1.67–12.77; P = 0.003) for those who had oral hairy leukoplakia. Conclusions: Oral manifestations occur commonly among HIV-infected Romanian children. Oral candidiasis and oral hairy leukoplakia were positive predictors of HIV disease progression.
Advances in Molecular Pathology and Treatment of Periampullary Cancers

Objectives Periampullary cancers (PACs) include the following 4 traditional anatomic subtypes: pancreatic, ampullary, biliary, or duodenal cancers. This review was performed to highlight recent advances in the genomic and molecular understanding of each PAC subtype and the advances in chemotherapeutic and molecular trials in these cancer subtypes. Results Recent advances have highlighted differences in the genomic and molecular features within each PAC subtype. Ampullary cancers can now be further defined accurately into their intestinal and pancreatobiliary subtypes using histomolecular profiling. K-ras mutation, which occurs in most pancreatic cancers, is found to occur less frequently in ampullary (42%–52%), biliary (22%–23%), and duodenal cancers (32%–35%), suggesting crucial differences in targetable mutations in these cancer subtypes. Ampullary cancers of intestinal subtype and duodenal cancers seem to share similarities with colorectal cancer, given that they respond to similar chemotherapeutic regimens. This has potential implications for clinical trials and treatment selection, where PACs are often considered together. Conclusions Future trials should be designed in view of our increased understanding of the different anatomic and histomolecularly profiled subtypes of PAC cancers, which respects their individual molecular characteristics, phenotype, and response to treatment.
Whole-Transcriptome and -Genome Analysis of Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates Identifies Downregulation of ethA as a Mechanism of Ethionamide Resistance

ABSTRACT Genetics-based drug susceptibility testing has improved the diagnosis of drug-resistant tuberculosis but is limited by our lack of knowledge of all resistance mechanisms. Next-generation sequencing has assisted in identifying the principal genetic mechanisms of resistance for many drugs, but a significant proportion of phenotypic drug resistance is unexplained genetically. Few studies have formally compared the transcriptomes of susceptible and resistant Mycobacterium tuberculosis strains. We carried out comparative whole-genome transcriptomics of extensively drug-resistant (XDR) clinical isolates using RNA sequencing (RNA-seq) to find novel transcription-mediated mechanisms of resistance. We identified a promoter mutation (t to c) at position −11 (t−11c) relative to the start codon of ethA that reduces the expression of a monooxygenase (EthA) that activates ethionamide. (In this article, nucleotide changes are lowercase and amino acid substitutions are uppercase.) Using a flow cytometry-based reporter assay, we show that the reduced transcription of ethA is not due to transcriptional repression by ethR. Clinical strains harboring this mutation were resistant to ethionamide. Other ethA promoter mutations were identified in a global genomic survey of resistant M. tuberculosis strains. These results demonstrate a new mechanism of ethionamide resistance that can cause high-level resistance when it is combined with other ethionamide resistance-conferring mutations. Our study revealed many other genes which were highly up- or downregulated in XDR strains, including a toxin-antitoxin module (mazF5 mazE5) and tRNAs (leuX and thrU). This suggests that global transcriptional modifications could contribute to resistance or the maintenance of bacterial fitness have also occurred in XDR strains.
Impact of different policies on unhealthy dietary behaviors in an urban adult population: an agent-based simulation model.

OBJECTIVES Unhealthy eating is a complex-system problem. We used agent-based modeling to examine the effects of different policies on unhealthy eating behaviors. METHODS We developed an agent-based simulation model to represent a synthetic population of adults in Pasadena, CA, and how they make dietary decisions. Data from the 2007 Food Attitudes and Behaviors Survey and other empirical studies were used to calibrate the parameters of the model. Simulations were performed to contrast the potential effects of various policies on the evolution of dietary decisions. RESULTS Our model showed that a 20% increase in taxes on fast foods would lower the probability of fast-food consumption by 3 percentage points, whereas improving the visibility of positive social norms by 10%, either through community-based or mass-media campaigns, could improve the consumption of fruits and vegetables by 7 percentage points and lower fast-food consumption by 6 percentage points. Zoning policies had no significant impact. CONCLUSIONS Interventions emphasizing healthy eating norms may be more effective than directly targeting food prices or regulating local food outlets. Agent-based modeling may be a useful tool for testing the population-level effects of various policies within complex systems.
Characterization of the Fawn-Hooded Rat as a Model for Hemostatic Studies

Summary A large colony of fawn-hooded (FH) rats, comprising five original families and six generations of their progeny, was developed for genetic and comparative studies of their bleeding tendency. The characteristics of the bleeding diathesis in these rats are similar to those originally reported in related rats by Tschopp and Zucker. FH rats have normal clot retraction, ADP-induced platelet aggregation and platelet ADP ; variable aggregation with collagen; minimal aggregation with adrenaline and cobra venom factor; and reduced platelet ATP, ATP/ADP ratio, serotonin content and 14C-serotonin release. In comparison to age- and sex-matched Wistar rats, FH rats have significantly prolonged partial thromboplastin time, shortened Russell’s viper venom time and increased factor X and XI levels. Other coagulation screening tests and specific assays for fibrinogen, plasminogen and factors VII, VIII and IX were normal. Some age- and sex-related differences in coagulation and other parameters were observed within each rat strain. Plasma proteins, glycoproteins and cerulo-plasmin (copper oxidase activity) showed no abnormalities, nor did initial studies of immunoglobulins and complement. However, FH rats have significantly lower glucose and higher cholesterol levels than comparable Wistar rats.
Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcription elongation.

Ternary complexes of RNA polymerase II, bearing the nascent RNA transcript, are intermediates in the synthesis of all eukaryotic mRNAs and are implicated as regulatory targets of factors that control RNA chain elongation and termination. Information as to the structure of such complexes is essential in understanding the catalytic and regulatory properties of the RNA polymerase. We have prepared complexes of purified RNA polymerase II halted at defined positions along a DNA template and used RNase footprinting to map interactions of the polymerase with the nascent RNA. Unexpectedly, the transcript is sensitive to cleavage by RNases A and T1 at positions as close as 3 nucleotides from the 3'-terminal growing point. Ternary complexes in which the transcript has been cleaved to give a short fragment can retain that fragment and remain active and able to continue elongation. Since DNA.RNA hybrid structures are completely resistant to cleavage under our reaction conditions, the results suggest that any DNA.RNA hybrid intermediate can extend for no more than 3 base pairs, in dramatic contrast to recent models for transcription elongation. At lower RNase concentrations, the transcript is protected from cleavage out to about 24 nucleotides from the 3' terminus. We interpret this partial protection as due to the presence of an RNA binding site on the polymerase that binds the nascent transcript during elongation, a model proposed earlier by several workers in preference to the hybrid model. The properties of this RNA binding site are likely to play a central role in the process of transcription elongation and termination and in their regulation.
A simple mechanism for financial bubbles: time-varying momentum horizon

Building on the notion that bubbles are transient self-fulfilling prophecies created by positive feedback mechanisms, we construct the simplest continuous price process whose expected returns and volatility are functions of momentum only. The momentum itself is measured by a simple continuous moving average of past prices over a given time horizon. We introduce a simple dynamics of the time horizon used by the representative investor, which is motivated by the race of trend following agents to forerun their competitors. We provide the full set of solutions, which includes an explosive regime where the price and momentum explodes stochastically in finite time to infinity, transient price dynamics escaping to infinity and recurrent behaviors, where the momentum remains either strictly positive or undergoes instantaneous reflections at the origin. The proposed price generating process produces price dynamics that are in agreement with the main qualitative properties of empirical financial time series. Moreover, it produces realistic regime shifts between non bubble and bubble regimes. We construct a quasi-likelihood methodology to calibrate the model to empirical financial time series, which is applied to an Internet index and a ‘brick and mortar’ index, over the period of the dotcom bubble and its subsequent crash, from Jan. 1998 to Dec. 2002. The Wilks test of nested hypotheses shows a very strong skill in diagnosing the bubble of the Internet index and in disqualifying a bubble in the ‘brick and mortar’ index.
Spatiotemporal Delivery Strategies for Promoting Musculoskeletal Tissue Regeneration

A primary regenerative medicine strategy is to stimulate or augment endogenous repair mechanisms that promote functional restoration of damaged or degenerated tissues. There is increasing evidence that maximizing the potency of tissue regenerative therapies will require design and development of delivery approaches that provide controlled spatiotemporal release of key signaling molecules. Guidance on which factors to deliver and the timing of delivery is emerging from advances in understanding of critical pathways involved in the development of integrated musculoskeletal tissues. A broad range of biomaterials‐based deployment technologies are becoming available that allow controlled spatial presentation and release kinetics of biological cues. The purpose of this perspective article is to review promising spatiotemporal delivery strategies designed to promote functional tissue regeneration with an emphasis on vascularized bone repair.
Bicycle equity in Brazil: Access to safe cycling routes across neighborhoods in Rio de Janeiro and Curitiba

ABSTRACT In many Latin American cities, rapid motorization and population growth have resulted in unprecedented urban transportation challenges, with lower income populations disproportionately facing constraints to mobility as well as externalities like air pollution, traffic collisions, and the impacts of climate change. The construction of bicycle lane networks has been identified as an effective tool for increasing citizen's mobility and accessibility as well as combating the effects of motorization, but in cities where bicycle lane networks exist, it is not known if they have benefited different income groups equally. This paper assesses the extent to which bicycle lane provisioning has been equitable among neighborhoods in Rio de Janeiro and Curitiba. Both cities were found to have more than twice the supply of bicycle lanes in the wealthiest quintile than the lowest income quintile relative to area and population. A network analysis using a Level of Traffic Stress classification to categorize roads found that wealthier areas have more commercial areas accessible along safer cycling routes. Implications for cycling policy and future research are discussed.
Entropy based noise clustering soft classification method for identification of wheat crop using time series MODIS data

In this study, time series MODIS-Terra MOD13Q1 data have been used for the identification of wheat crop in a test site in the state of Haryana in India. Wheat is the dominating crop in this region having large and homogeneous fields. A total of seven date data have been taken between November 2011 to April 2012, corresponding to the different phenological stages of wheat crop of this study area. The Normalized Difference Vegetation Index (NDVI) and Soil Adjusted Vegetation Index (SAVI) have been generated for each date MODIS data. Further, these indices were then used to make the temporal indices sets. The Transformed Divergence (TD) separability based optimized sets of temporal spectral indices were then used for classification of wheat crop using the supervised entropy based noise clustering soft classification algorithm. For the assessment of accuracy the Receiver Operating Characteristic (ROC) analysis has been used. It is observed that the highest area under ROC curve is found for NDVI `Three' date temporal dataset combination, which is a combination of sowing, flowering and maturity stages of wheat phenology. Further, the inclusions of milking stage and maturity stage data has decreased the accuracy. Thus, it may be concluded that `Three' date combination of NDVI generated from MODIS yields best result for identification of wheat crop using entropy based noise clustering classifier.
An unsupervised learning framework for discovering the site-specific ontology from multiple Web pages

We develop an unsupervised learning framework for tackling the problem of automatic site-specific ontology discovery from multiple pages of a Web site. To harness the uncertainty involved, our framework is designed based on a generative model which models the generation of text fragments contained in the pages of a Web site. One characteristic of our framework is that we consider clues from multiple pages collected from the Web site. Another characteristic is that we learn the regularities of the layout format to discover the site-specific ontology via stochastic grammatical inference. To accomplish the goal of ontology discovery, the ontology information blocks of a Web page are identified by making use of the site invariant information. We have conducted extensive experiments using real-world Web sites. Comparisons between existing methods and our framework have been carried out to demonstrate the effectiveness of our framework.
Georgia from National Awakening to Rose Revolution: Delayed Transition in the Former Soviet Union

Contents: Map of Georgia's Provinces Actors and structures: the anatomy and evolution of regimes The Soviet legacy: implications for regime change Nationalist mobilization in Georgia 1989-1991 Shevardnadze's return and its aftermath 1992-1995 Profile of a corrupt regime: the Georgian State 1996-2001 Pressure from below: the influence of society on the Georgian State 1996-2001 The 'Rose Revolution': a second transition? Conclusion Appendix Bibliography Index.
Comparison of wrist blood pressure measurement with conventional sphygmomanometry at a cardiology outpatient clinic

Objective Oscillometric measurement of blood pressure at the wrist is becoming a widely used method for detection of hypertension and its control by treatment. The objective of the present study was to evaluate accuracy and suitability of wrist measurement in a clinical routine setting. Patients and methods A series of 333 consecutive patients admitted to our cardiology outpatient clinic were included. Blood pressure was measured at both upper arms according to World Health Organization–International Society of Hypertension guidelines. Oscillometric measurement was performed at the contralateral wrist simultaneously. Blood pressure readings were taken by an oscillometric device applied at the wrist (‘Klock’; Industrielle Entwicklung Medizintechnik, Stolberg, Germany) and a conventional mercury sphygmomanometer applied at the upper arm. Results Seventy-eight patients were excluded due to differences in blood pressure > 5 mmHg between both upper arms or due to ‘error’ messages of the wrist device. The data of the remaining 255 patients (149 males; mean age, 65 ± 13 years; range, 18–95 years) are presented. Mean conventional blood pressure was significantly lower compared with the wrist device (137 ± 20/80 ± 11 mmHg versus 153 ± 28/87 ± 18 mmHg; P < 0.001 and P < 0.001). The mean difference was 16 ± 25/6 ± 17 mmHg. In clinical terms, differences in blood pressure exceeding ±20/±10 mmHg reflecting classification of hypertension are considered important. Measurements of 101 (40%) patients were within these limits. Systolic readings of 110 (43%) and diastolic readings of 117 patients (46%) were beyond this scope. Conclusion Due to low reliability of wrist blood pressure measurement, it cannot compete with the upper arm standard procedure. If ever, it should only be used if test readings in an individual comparing wrist and upper arm measurement show differences within a range of ±20/±10 mmHg.
Security in Social Networking Services: A Value-Focused Thinking Exploration in Understanding Users’ Privacy and Security Concerns

The continued growth of Social Networking Services (SNS) has significant implications for computer and cybercrime management. In exploring the human side of security, studies have shown that any security response requires more than technical solutions. This is even more so as users are often seen as the main point of vulnerabilities for computer systems including SNS. This study seeks to probe the important values in understanding how to maximize end-user security and privacy concerns in SNS. The study applies the Value-focused Thinking methodology to uncover the SNS users’ values in the form of their fundamental objectives/wishes, with an initial focus on developing economies in the Caribbean. The study found that privacy and integrity of SNS, security controls, corporate social responsibility and personal responsibility are fundamental in maximizing user security and privacy.
Aragonite crystallization in primary cell cultures of multicellular isolates from a hard coral, Pocillopora damicornis

The foundation of marine coral reef ecosystems is calcium carbonate accumulated primarily by the action of hard corals (Coelenterata: Anthozoa: Scleractinia). Colonial hard coral polyps cover the surface of the reef and deposit calcium carbonate as the aragonite polymorph, stabilized into a continuous calcareous skeleton. Scleractinian coral skeleton composition and architecture are well documented; however, the cellular mechanisms of calcification are poorly understood. There is little information on the nature of the coral cell types involved or their cooperation in biocalcification. We report aragonite crystallization in primary cell cultures of a hard coral, Pocillopora damicornis. Cells of apical coral colony fragments were isolated by spontaneous in vitro dissociation. Single dissociated cell types were separated by density in a discontinuous Percoll gradient. Primary cell cultures displayed a transient increase in alkaline phosphatase (ALP) activity, to the level observed in intact corals. In adherent multicellular isolate cultures, enzyme activation was followed by precipitation of aragonite. Modification of the ionic formulation of the medium prolonged maintenance of isolates, delayed ALP activation, and delayed aragonite precipitation. These results demonstrate that in vitro crystallization of aragonite in coral cell cultures is possible, and provides an innovative approach to investigate reef-building coral calcification at the cellular level.
How chaperones fold proteins.

Chaperones are a functionally related group of proteins assisting protein folding in the cell under physiological and stress conditions. They share the ability to recognize and bind nonnative proteins thus preventing unspecific aggregation. The underlying functional principles of the different chaperone classes are beginning to be understood. A landmark feature of molecular chaperones is the involvement of energy-dependent reactions in the folding process. Nucleotide binding to ATP-dependent chaperones (e.g. GroEL, Hsp70, Hsp90) leads to sometimes large conformational changes in the chaperone which allow to shift between high- and low-affinity states for substrate proteins. Interestingly, the ATPase activity which is the key determinant for functional cycles is tightly regulated by a set of co-chaperones. While for ATP-dependent chaperones binding sites for nucleotide and protein are found in one protein, in the case of ATP-independent chaperones (e. g. sHsps, SecB) the energy-dependent step is performed by another chaperone (Hsp70, SecA). Therefore, the ATP-independent chaperones can be regarded as efficient 'holding' components. Cooperation of different chaperone machineries creates a synergistic network of folding helpers in the cell, which allows to maintain protein homeostasis under conditions nonpermissive for spontaneous folding.
Modelling tourist flow association for tourism demand forecasting

The purpose of this study is to examine tourism demand for Singapore from 1995 to 2013 by six major origin countries which belong to three different regions. Unlike prior tourism research, we take into account the dependence relations among the different tourist flows via copula. Copula is a statistical model of dependence and measurement of association. Specifically, we investigate the association between two tourist flows in each region. Based on empirical copula estimation, the Frank function has been identified as the most appropriate to capture the pairwise dependence structures of tourist flows. The copula-based approach combined with econometric models is proposed for tourism demand analysis that can be used to predict tourist arrivals. We apply the copula-ARDL and copula-ECM frameworks to generate joint forecasts of tourist arrivals from three regions. The findings show that the forecast performance of the Frank copula-based model outperforms the benchmark model which corresponds to the independence structure (no association) of tourist flows.