Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficiencies of Four Versions of the AMPLICOR HIV-1 MONITOR Test for Quantification of Different Subtypes of Human Immunodeficiency Virus Type 1

ABSTRACT Three versions of a commercial human immunodeficiency virus (HIV) type 1 (HIV-1) load test (the AMPLICOR HIV-1 MONITOR Test versions 1.0, 1.0+, and 1.5; Roche Diagnostics, Branchburg, N.J.) were evaluated for their ability to detect and quantify HIV-1 RNA of different genetic subtypes. Plasma samples from 96 patients infected with various subtypes of HIV-1 (55 patients infected with subtype A, 9 with subtype B, 21 with subtype C, 2 with subtype D, 7 with subtype E, and 2 with subtype G) and cultured virus from 29 HIV-1 reference strains (3 of subtype A, 6 of subtype B, 5 of subtype C, 3 of subtype D, 8 of subtype E, 3 of subtype F, and 1 of subtype G) were tested. Detection of subtypes A and E was significantly improved with versions 1.0+ and 1.5 compared to that with version 1.0, whereas detection of subtypes B, C, D, and G was equivalent with the three versions. Versions 1.0, 1.0+, and 1.5 detected 65, 98, and 100% of the subtype A-infected samples from patients, respectively, and 71, 100, and 100% of the subtype E-infected samples from patients, respectively. Version 1.5 yielded a significant increase in viral load for samples infected with subtypes A and E (greater than 1 log10 HIV RNA copies/ml). For samples infected with subtype B, C, and D and tested with version 1.5, only a slight increase in viral load was observed (<0.5 log10). We also evaluated a prototype automated version of the test that uses the same PCR primers as version 1.5. The results with the prototype automated test were highly correlated with those of the version 1.5 test for all subtypes, but were lower overall. The AMPLICOR HIV-1 MONITOR Test, version 1.5, yielded accurate measurement of the HIV load for all HIV-1 subtypes tested, which should allow the test to be used to assess disease prognosis and response to antiretroviral treatment in patients infected with a group M HIV-1 subtype.
Comparative gene mapping: cytogenetic localization of PROC, EN1, ALPI, TNP1, and IL1B in cattle and sheep reveals a conserved rearrangement relative to the human genome

The cytogenetic locations of the genes for protein C (PROC), transition protein 1 (TNP1), intestinal alkaline phosphatase (ALPI), engrailed (EN1), and human protointerleukin β (IL1B) have been compared between cattle (Bos taurus, BTA) and sheep (Ovis aries, OAR). Bovine YAC and cosmid clones were used as FISH probes to determine the order (centromere to telomere) of four of these genes on OAR 2q, as well as the location of IL1B on OAR 3p. In cattle, IL1B and EN1 were assigned to BTA 11 and BTA 2, respectively. Alignment of the ovine, bovine, and human physical maps based on these data shows that segments of conserved synteny and chromosomal rearrangements detected between cattle and human are also found in sheep, where the order in cattle is conserved.
A Survey on Thyroid Hormonal Status among Moderate to Severe Stable Chronic Obstructive Pulmonary Disease

Background : COPD is one of the common diseases in pulmonary medicine. Current knowledge indicated that there was a link between COPD with thyroid hormonal abnormalities. Thyroid function disturbances can be able to affect on the COPD through upper airway obstruction,respiratory muscle weakness, development of central and obstructive sleep apnea,alveolar hypoventilation, and pleural effusion. Thyroid abnormalities are often both detectable and treatable. The aim of the study is to assessserum levels of thyroid hormones among moderate to severe stable COPD patients. Methods: 34 men were enrolled consecutive among established and stable COPD patients with moderate to the severe stages. Their selection constructed on the ATS/GOLD guidelines. Thyroid functions and hormonal concentrations measured according to manufacturer's instructions. Results: Mean age of sample was 51.7±5.76SD years. It ranged over 42–60 years (Mode=49). Significant thyroid hormonal abnormalities were detected among established moderate to the severe COPD patients. The mean±SD of TSH, TT4 and free T3 concentrations in the focus population was 2.36±1.53 microIU/ml, 12.15±2.15 Micro/dl and 2.20±0.45 pg/ml, respectively. Frequency distribution of thyroid disorders included euthyroid functions 76.5%; three subjects of those had euthyroid sick syndrome, subclinical hyperthyroidism 20.6% and over hypothyroidism 2.9%, respectively. Grades of goiter on WHO classifications observed 0=44% and 1=41%. Conclusion: Frequent exacerbations of thyroid disorders were detected among stable, moderate to severe COPD patients. Subclinical hyperthyroidism and euthyroid sick syndrome were significant. Despite that prevalence of hypothyroidism is considerable in age-rang of Iranian’s population.
To Evaluate the Correlation Between Skeletal and Dental Parameters to the Amount of Crowding in Class II Div. 1 Malocclusions.

Introduction Crowding of teeth is one of the most common problem that motivates the patient to seek orthodontic treatment. Determination of etiology of crowding could have a significant effect on treatment planning and prognosis of Class II malocclusion. Aim Aim of this study was to evaluate the relationship of skeletal and dental parameters to amount of dental crowding in patients with Class II Divison 1 (div.1) malocclusion. Materials and Methods Pretreatment lateral cephalograms and dental casts of 60 patients with skeletal Class II malocclusion were collected for the study. The sample was divided into two groups according to severity of pretreatment mandibular crowding. Group I consisted of cases with crowding ≥3 mm and Group II with crowding <3 mm. Lateral cephalograms for each patient was manually traced and skeletal parameters (effective maxillary and mandibular length, mandibular plane angle, Y Axis, lower anterior face height) and dental parameters (axial inclination of lower incisor, inclination of lower incisor to mandibular plane, interincisal angle) were measured. Unpaired t-test was used for intergroup comparison and relationship between different measurements was investigated using Pearson correlation coefficient. Results Among the skeletal parameters measured, only effective mandibular length exhibited statistically significant difference between the two groups. No statistically significant difference was found between the two groups for any of the dental parameters. Significant inverse correlation was found between mandibular crowding and effective mandibular length. Conclusion Subjects with Class II div.1 malocclusion and moderate to severe mandibular crowding have significantly smaller effective mandibular base length than subjects with the same malocclusion and slight mandibular crowding.
Novel landmark-guided routes in ants

SUMMARY We review studies in which ants familiar with fixed routes between their nest and a feeding site are displaced from one of these destinations to an unfamiliar site away from the route. Ants can reach their goal from such novel release sites guided by distant landmarks. We suggest that an ant's ability to take such novel landmark-guided routes after displacement is a by-product of the robustness of normal route-following and is unlikely to reflect the ant's use of a map-like knowledge of its surroundings.
Antimony-resistant but not antimony-sensitive Leishmania donovani up-regulates host IL-10 to overexpress multidrug-resistant protein 1

The molecular mechanism of antimony-resistant Leishmania donovani (SbRLD)–driven up-regulation of IL-10 and multidrug-resistant protein 1 (MDR1) in infected macrophages (Mϕs) has been investigated. This study showed that both promastigote and amastigote forms of SbRLD, but not the antimony-sensitive form of LD, express a unique glycan with N-acetylgalactosamine as a terminal sugar. Removal of it either by enzyme treatment or by knocking down the relevant enzyme, galactosyltransferase in SbRLD (KD SbRLD), compromises the ability to induce the above effects. Infection of Mϕs with KD SbRLD enhanced the sensitivity toward antimonials compared with infection with SbRLD, and infection of BALB/c mice with KD SbRLD caused significantly less organ parasite burden compared with infection induced by SbRLD. The innate immune receptor, Toll-like receptor 2/6 heterodimer, is exploited by SbRLD to activate ERK and nuclear translocation of NF-κB involving p50/c-Rel leading to IL-10 induction, whereas MDR1 up-regulation is mediated by PI3K/Akt and the JNK pathway. Interestingly both recombinant IL-10 and SbRLD up-regulate MDR1 in Mϕ with different time kinetics, where phosphorylation of PI3K was noted at 12 h and 48 h, respectively, but Mϕs derived from IL-10−/− mice are unable to show MDR1 up-regulation on infection with SbRLD. Thus, it is very likely that an IL-10 surge is a prerequisite for MDR1 up-regulation. The transcription factor important for IL-10–driven MDR1 up-regulation is c-Fos/c-Jun and not NF-κB, as evident from studies with pharmacological inhibitors and promoter mapping with deletion constructs.
Pseudo Random Alteration of Sequence Numbers (PRAS): A novel method for defending sessiion hijacking attack in mobile adhoc network

TCP attacks are the major problem faced by Mobile Ad hoc Networks (MANETs) due to its limited network and host resources. Although the session hijacking is not in the forefront of everyone mind, it still remains a commonly used attack in MANET. Session hijack attacks are defined as taking over an active TCP/IP communication session without their permission or knowledge. When implemented successfully, attackers assume the identity of the compromised user, enjoying the same access to resources as the compromised user. Network protocols like FTP, Telnet, and rlogin are especially attractive to the attacker, because of the session oriented nature of their connections, and lack of implementation of any security during login, authentication, or data transmission. We introduce a novel method for defending session hijacking attack in MANET: Pseudo Random Alteration of Sequence Numbers (PRAS). Based on the comprehensive evaluation based on simulations, it is shown that PRAS can successfully defend session hijacking under diverse mobile multi-hop network environment with low communication, computation, and memory overhead.
A knowledge representation model for massive open online course platforms

This paper describes a knowledge model for the design of Massive Open Online Course (MOOC) platforms. It is based on our generic instructional engineering method called Knowledge Field of Educational Environment with Competence Boundary Conditions (KFEEC). KFEEC uses the ontology as a foundation for the knowledge representation model. It provides a flexible structure to the various self-paced e-learning system designs but appears to be overcomplicated for the MOOC platform. This paper describes the KFEEC method, the steps of adapting the KFEEC to the MOOC platform design, and the specification of the resulting knowledge model. This model is a core of the MOOC platform that will be developed in future work.
NOSER: An algorithm for solving the inverse conductivity problem

The inverse conductivity problem is the mathematical problem that must be solved in order for electrical impedance tomography systems to be able to make images. Here we show how this inverse conductivity problem is related to a number of other inverse problem. We then explain the workings of an algorithm that we have used to make images from electrical impedance data measured on the boundary of a circle in two dimensions. This algorithm is based on the method of least squares. It takes one step of a Newton's method, using a constant conductivity as an initial guess. Most of the calculations can therefore be done analytically. The resulting code is named NOSER, for Newton's One‐Step Error Reconstructor. It provides a reconstruction with 496 degrees of freedom. The code does not reproduce the conductivity accurately (unless it differs very little from a constant), but it yields useful images. This is illustrated by images reconstructed from numerical and experimental data, including data from a human chest.
Quantitative research for improving respiratory muscle contraction by breathing exercise.

OBJECTIVE To investigate the effects of breathing exercise on chronic obstructive pulmonary disease (COPD). PATIENTS AND METHODS 324 patients stable COPD were randomly assigned to either the breathing exercise group (Group I) or control group consisting of placebo (Group II). The maximum respiratory pressure (320 cases) and transdiaphragmatic pressure (129 cases) were monitored via RMS-I and Type-2 pressure measurements. The breathing exercises were taught and checked by experienced specialists periodically. Comparison was made between Group I and Group II using maximum inspiratory pressure (MIP), maximum expiratory pressure (MEP), diaphragmatic pressure (Pdi) and maximum transdiaphragmatic pressure (Pdimax) after 1 to 20 months. RESULTS In Group I MIP increased by 30.42%, MEP 32.10%, Pdi 30.94% and Pdimax 65.59% (P < 0.001). No significant changes were observed in Group II given the placebo. The MIP, MEP, Pdi and Pdimax were 6.95%, 2.92%, 14.63 and 9.05% respectively (P > 0.05). CONCLUSIONS Breathing exercise has a potent and long lasting effect on respiratory muscle contraction. The methods mentioned above can be used as standard quantitative index for contractile properties of respiratory muscle.
Weight bias in 2001 versus 2013: Contradictory attitudes among obesity researchers and health professionals

To assess levels of two types of anti‐fat bias in obesity specialists, explicit bias, or consciously accessible anti‐fat attitudes, and implicit bias, or attitudes that are activated outside of conscious awareness, were examined. This study also assessed changes over time by comparing levels of bias in 2013 to published data from 2001.
Association of Magnetic Resonance Imaging Markers of Cerebrovascular Disease Burden and Cognition

Background and Purpose— The present study sought to examine the association between the burden of cerebrovascular disease (CeVD) as assessed by multimodal magnetic resonance imaging and neurocognitive function. Methods— Cognitively impaired patients and controls were tested on an extensive neuropsychological battery and underwent multimodal brain magnetic resonance imaging. CeVD markers determined from magnetic resonance imaging included the presence of multiple lacunes, multiple cerebral microbleeds, and moderate or severe white matter hyperintensities as markers for small-vessel disease and cortical stroke and intracranial stenosis as markers for large-vessel disease. A weighted CeVD burden score was constructed, and its association with global and domain-specific cognitive performance was investigated. Results— A total of 305 cases and 94 controls were included in the analysis. A graded association of CeVD burden with neurocognitive function was found. Moreover, a clear threshold of CeVD burden was associated with severe impairment. White matter hyperintensities was associated with global neurocognitive deficits, whereas microbleeds were associated with domain-specific impairments. Conclusions— The weighted CeVD burden score comprising markers of both small- and large-vessel diseases were associated with deficits in both global and domain-specific neurocognitive function. Additional studies are needed to validate the use of this CeVD burden score for the prediction of dementia.
Microphysical particle parameters from extinction and backscatter lidar data by inversion with regularization: theory.

A method is proposed that permits one to retrieve physical parameters of tropospheric particle size distributions, e.g., effective radius, volume, surface-area, and number concentrations, as well as the mean complex refractive index on a routine basis from backscatter and extinction coefficients at multiple wavelengths. The optical data in terms of vertical profiles are derived from multiple-wavelength lidar measurements at 355, 400, 532, 710, 800, and 1064 nm for backscatter data and 355 and 532 nm for extinction data. The algorithm is based on the concept of inversion with regularization. Regularization is performed by generalized cross-validation. This method does not require knowledge of the shape of the particle size distribution and can handle measurement errors of the order of 20%. It is shown that at least two extinction data are necessary to retrieve the particle parameters to an acceptable accuracy. Simulations with monomodal and bimodal logarithmic-normal size distributions show that it is possible to derive effective radius, volume, and surface-area concentrations to an accuracy of +/-50%, the real part of the complex refractive index to +/-0.05, and the imaginary part to +/-50%. Number concentrations may have errors larger than +/-50%.
Nonlinear dynamics of twisted and coiled polymer actuator made of conductive nylon based on the energy balance

This paper proposes a novel dynamics model of the twisted and coiled polymer actuator (TCPA) which is one of the artificial muscles recently discovered. It can be driven by Joule heating and can contract up to 25%. Most of the conventional works employed the linear model of TCPA which represents the relationships between the input voltage, the temperature, and the displacement, but the real TCPA shows the nonlinearity. Although a nonlinear model was proposed based on the curve fitting, it is difficult to apply the model to the various TCPAs. Additionally, the conventional works cannot explain the effect of the convective heat transfer condition on the displacement behavior of TCPA. This paper aims to construct a general nonlinear model of TCPA based on the following two ideas: (1) The energy balance of TCPA and (2) the temperature and velocity dependence of the heat transfer coefficient. The temperature model is obtained from the time derivative of the energy balance, and the displacement model is derived as Lagrange's equation of motion with the dissipation function. Through experiments, it is verified that the proposed model is closer to the real dynamics than the conventional linear model.
Preferential Infection of Immature Dendritic Cells and B Cells by Mouse Mammary Tumor Virus1

Until now it was thought that the retrovirus mouse mammary tumor virus preferentially infects B cells, which thereafter proliferate and differentiate due to superantigen-mediated T cell help. We describe in this study that dendritic cells are infectable at levels comparable to B cells in the first days after virus injection. Moreover, IgM knockout mice have chronically deleted superantigen-reactive T cells after MMTV injection, indicating that superantigen presentation by dendritic cells is sufficient for T cell deletion. In both subsets initially only few cells were infected, but there was an exponential increase in numbers of infected B cells due to superantigen-mediated T cell help, explaining that at the peak of the response infection is almost exclusively found in B cells. The level of infection in vivo was below 1 in 1000 dendritic cells or B cells. Infection levels in freshly isolated dendritic cells from spleen, Langerhans cells from skin, or bone marrow-derived dendritic cells were compared in an in vitro infection assay. Immature dendritic cells such as Langerhans cells or bone marrow-derived dendritic cells were infected 10- to 30-fold more efficiently than mature splenic dendritic cells. Bone marrow-derived dendritic cells carrying an endogenous mouse mammary tumor virus superantigen were highly efficient at inducing a superantigen response in vivo. These results highlight the importance of professional APC and efficient T cell priming for the establishment of a persistent infection by mouse mammary tumor virus.
Cochrane Systematic Review of Colorectal Cancer Screening Using the Fecal Occult Blood Test (Hemoccult): An Update

BACKGROUND AND AIMS:Reducing mortality from colorectal cancer (CRC) may be achieved by the introduction of population-based screening programs. The aim of the systematic review was to update previous research to determine whether screening for CRC using the fecal occult blood test (FOBT) reduces CRC mortality and to consider the benefits, harms, and potential consequences of screening.METHODS:We searched eight electronic databases (Cochrane Library, MEDLINE, EMBASE, CINAHL, PsychINFO, AMED, SIGLE, and HMIC). We identified nine articles describing four randomized controlled trials (RCTs) involving over 320,000 participants with follow-up ranging from 8 to 18 yr. The primary analyses used intention to screen and a secondary analysis adjusted for nonattendance. We calculated the relative risks and risk differences for each trial, and then overall, using fixed and random effects models.RESULTS:Combined results from the four eligible RCTs indicated that screening had a 16% reduction in the relative risk (RR) of CRC mortality (RR 0.84, 95% confidence interval [CI] 0.78–0.90). There was a 15% RR reduction (RR 0.85, 95% CI 0.78–0.92) in CRC mortality for studies that used biennial screening. When adjusted for screening attendance in the individual studies, there was a 25% RR reduction (RR 0.75, 95% CI 0.66–0.84) for those attending at least one round of screening using the FOBT. There was no difference in all-cause mortality (RR 1.00, 95% CI 0.99–1.02) or all-cause mortality excluding CRC (RR 1.01, 95% CI 1.00–1.03). CONCLUSIONS:The present review includes seven new publications and unpublished data concerning CRC screening using FOBT. This review confirms previous research demonstrating that FOBT screening reduces the risk of CRC mortality. The results also indicate that there is no difference in all-cause mortality between the screened and nonscreened populations.
Pulmonary arterial pressure and electrocardiograms in broiler chickens infused intravenously with L-NAME, an inhibitor of nitric oxide synthase, or sodium nitroprusside (SNP), a nitric oxide donor

1. Broilers were divided at 42 to 44 d of age into a Control group ( n =30) and a Treatment group ( n =30). The mean pulmonary arterial pressure (mPAP) and electrocardiogram (ECG) leads II and aV F were measured 1, 2 and 4 h after an intravenous injection of 0.9% saline (Control group) or Nω -nitro-L-arginine methyl esther (L-NAME), an inhibitor of nitric oxide synthase and thus an inhibitor of endothelial nitric oxide (NO) production (Treatment group). 2. At 1 and 2 h but not 4 h post-injection, L-NAME significantly increased the mPAP and the amplitudes of the ECG S-wave and RS-wave leads II and aV F when compared with Control values. 3. The correlation coefficients between the mPAP and the ECG S-wave and RS-wave amplitudes for lead II within the Treatment group were-0.848 and-0.553 at 1 h and-0.798 and-0.512 at 2 h, respectively. The corresponding coefficients for lead aV F were-0.735, -0.596, -0.663 and-0.724, respectively. 4. After suitable mPAP and ECG values had been recorded at each time interval, sodium nitroprusside (SNP), which acts as a short-lived NO donor molecule, was injected intravenously via a right-cardiac catheter. Within 5 min after the SNP injection, the mPAP and the ECG lead II S-wave and RSwave amplitudes were transiently reduced to levels that, at 1 and 2 h after L-NAME injection, did not differ from Control values. Within 10 min after the SNP injection, all values returned to the levels previously induced by L-NAME. 5. These results demonstrate that L-NAME increased the myocardial contractility and PAP, whereas SNP transiently reversed the effects of L-NAME on myocardial contractility and PAP. It appears likely from these results that the pulmonary vascular endothelium releases NO that in turn reduces the pulmonary vascular resistance or attenuates myocardial contractility in broiler chickens.