Miracle-dz/UniFAR-FTUs huggingface dataset:
Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection

Objective To measure HIV-1 quasispecies diversity in very recently infected male and female plasma donors. Methods HIV-1 RNA testing of blood and plasma donations was used to select anti HIV-1 antibody negative, HIV-1 RNA positive plasma samples from 13 males and four females undergoing primary infection. To determine whether these early viral populations were clonal or oligoclonal, heteroduplex mobility assays were performed on multiple independently generated envelope PCR products. Genetically heterogeneous quasispecies where subcloned and their divergent envelope variants sequenced. Results Because of frequent plasma donations in this population, HIV-1 RNA quasispecies could be studied during very early primary infection. Heteroduplex mobility assays detected the presence of genetically distinct variants in four of the 17 plasma donors. DNA sequence analysis showed that one case was due to a G to A hyper-mutation event and that two cases were caused by the presence of in-frame insertions/deletions resulting in DNA heteroduplex mobility shifts. The early plasma quasispecies of one female contained highly divergent variants differing by up to 6% substitution and multiple insertions/deletions, a level of divergence unlikely to have been generated de novo following transmission. V3 loop sequences analysis indicated the presence of non-syncitium inducing genotypes in 14 out of 17 primary infection cases. Conclusion Plasma viremia is generally genetically homogeneous even during the very early phase of primary infection when viremia is first detected and still rising exponentially. Evidence for the transmission of multiple variants was detected in only one out of four women and none of 13 men undergoing primary infection with subtype B HIV-1.
Immune enhancement of pulmonary bactericidal activity in murine virus pneumonia.

Bacterial multiplication in the lung associated with murine Sendai virus pneumonia is caused by virus-induced defects in pulmonary bactericidal mechanisms. The nature of this effect has been studied in animals immunized against the challenge bacteria. Mice were immunized against Proteus mirabilis by intraperitoneal inoculation and by aerosol inhalation. After the development of immunity, mice were infected aerogenically with 10(4) TCID(50) of Sendai virus. 7 days later, during the height of the bronchial inflammation and pulmonary consolidation, the mice were challenged with an aerosol of viable (35)S-labeled Proteus mirabilis or (32)P-labeled Staphylococcus aureus.Nonimmunized virus-infected animals showed marked impairment of pulmonary bactericidal activity with subsequent multiplication of the bacterial strain in the case of Proteus mirabilis. Immunized nonvirus-infected animals showed enhancement of pulmonary bactericidal activity for the homologous and heterologous strains in comparison with nonimmunized animals. Virus-infected animals immunized by aerosol showed enhanced bactericidal activity against the homologous but not the heterologous bacterial strain. Neither virus infection nor immunization had a significant effect on the transport of particles in the lung. The data demonstrated that the bacterial multiplication associated with the virus pneumonia was prevented by preceding immunization against the homologous challenge organism. The data suggest a mechanism for controlling bacterial multiplication associated with virus pneumonias.
MRI as an outcome in multiple sclerosis clinical trials

Introduction: T2-weighted and gadolinium enhanced T1-weighted MRI scans measure plaque burden and breakdown of the blood-brain barrier, respectively, in multiple sclerosis (MS) lesions. These have become widely used outcome measures for monitoring disease activity in clinical trials and clinical practice. However, their use as surrogates or biomarkers for disability and relapses, key clinical outcome measures, has remained incompletely validated. Methods: In a clinical trial database comprised of 31 relapsing-remitting and secondary progressive MS trial placebo groups, we assessed relationships between 1) T2 lesion load (TLL) change and disability change and 2) gadolinium enhancement of MS lesions and on-study relapses with univariate and multivariate analyses. Results: In relapsing-remitting MS, TLL change (n = 223) made no independent contribution to predicting change in disability from baseline to trials’ end. Similarly, inclusion of gadolinium enhancing lesions (n = 170) into multivariate models did not independently contribute to the predictive value for on-trial relapses. In secondary progressive MS, a small effect of TLL was found for disability change (n = 355) but in multivariate analysis this accounted for less than 5% of the variance in end-of-trial disability. Results were replicated in independent datasets, more than doubling effective sample sizes. Conclusions: MRI measures widely used in trials of relapsing-remitting and progressive multiple sclerosis add little if anything independently to the clinically relevant relapse and disability outcomes. These results reemphasize the importance of validating potential surrogate markers against clinical measures and highlight the need for better MRI markers of disease activity and progression. AIC = Akaike’s information criterion; EDSS = Expanded Disability Status Scale; LME = linear mixed effects; MS = multiple sclerosis; RCT = randomized clinical trial; RRMS = relapsing-remitting MS; SLC = Sylvia Lawry Centre; SPMS = secondary progressive MS; TLL = T2 lesion load.
Changing scenario of cryptococcosis in a tertiary care hospital in north India.

BACKGROUND & OBJECTIVES With the increase in the number of patients of AIDS, the incidence of cryptococcosis is on the rise in India. It was therefore considered important to evaluate the predisposing factors, laboratory investigations and outcome of patients with cryptococcosis in this changed scenario. METHODS We assessed 58 patients with cryptococcosis retrospectively over a five year period (January 1995-December 1999) at the Nehru Hospital, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh. RESULTS The annual incidence of cryptococcosis in PGIMER, Chandigarh has increased about 15 fold from 1970-1982 (pre AIDS era) to 1995-1999 (present series). Of the 47 patients studied for predisposing factors, 36 patients were identified with predisposing factors, HIV infection (57.4%) was the commonest followed by haematologic malignancies (6.3%) and renal transplant (4.2%). Forty one patients were diagnosed by isolation of the organism as well as antigen detection in cerebrospinal fluid/serum, 9 by isolation alone and 8 by antigen detection alone. Quantitative antigen titres were done in 38 patients and a significantly higher (P < 0.01) antigen titre (> 512) was observed in HIV positive patients as compared to HIV negative patients. All isolates tested were of Cryptococcous neoformans var neoformans biotype and no resistance to antifungal agents was noted. Twenty of 41 patients receiving treatment improved. The results were compared with other studies available from India. INTERPRETATION & CONCLUSION The incidence of cryptococcosis is on the rise in this part of north India and this can be attributed to an increase in AIDS cases.
Active toroid nano antenna excited by an circular polarized plane wave

A novel toroid-structured coated nano particle (T-CNP) antenna with an active core (doped with rare earth ion Er3+) is studied in this paper. It is demonstrated that the active toroid-structured nano particle, when illuminated by a circular polarized plane wave, acts as a strong radiator at its resonant frequency (around 600 THz).
Screening merits of the Lang II, Frisby, Randot, Titmus, and TNO stereo tests.

PURPOSE Previous works show a pronounced disagreement on the reliability of stereo tests as screening tools for amblyopia and strabismus. This study's aim was to compare the ability of the Lang II, Frisby, Randot, Titmus, and TNO stereo tests to detect amblyopia and strabismus with visual acuity testing and cover testing. METHODS A total of 1035 school children aged 12 to 13 years were examined in a field study in Monterrey, Mexico. In addition to the 5 stereo tests, the examination included visual acuity, cover testing, refraction (skiascopy), and inspection of the red reflex and posterior pole. RESULTS Sensitivity ranged from 17% to 47% (Frisby-Titmus-Lang II-Randot-TNO, in order of occurrence). Of the 60 subjects with strabismus and/or amblyopia, only 8 subjects were identified by all 5 stereo tests. A considerable number of subjects (25), the majority of whom were amblyopic (23 subjects), were not identified by any of the tests. All stereo tests showed higher sensitivities for strabismus than for amblyopia. CONCLUSION None of the 5 stereo tests studied is suitable for screening for amblyopia or strabismus. The results of both ocularly normal subjects and subjects with strabismus and/or amblyopia are variable, and there is no way of separating normal response from abnormal response.
Nucleotide Variability and Translation Efficiency of the 5′ Untranslated Region of Hepatitis A Virus: Update from Clinical Isolates Associated with Mild and Severe Hepatitis

ABSTRACT Mutations in the internal ribosome entry site (IRES) of hepatitis A virus (HAV) have been associated with enhanced in vitro replication and viral attenuation in animal models. To address the possible role of IRES variability in clinical presentation, IRES sequences were obtained from HAV isolates associated with benign (n = 8) or severe (n = 4) hepatitis. IRES activity was assessed using a bicistronic dual-luciferase expression system in adenocarcinoma (HeLa) and hepatoma (HuH7) cell lines. Activity was higher in HuH7 than in HeLa cells, except for an infrequently isolated genotype IIA strain. Though globally low, significant variation in IRES-dependent translation efficiency was observed between field isolates, reflecting the low but significant genetic variability of this region (94.2% ± 0.5% nucleotide identity). No mutation was exclusive of benign or severe hepatitis, and variations in IRES activity were not associated with a clinical phenotype, indirectly supporting the preponderance of host factors in determining the clinical presentation.
Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis[W]

This work presents a machine learning–based method for transcriptome analysis via comparison of gene coexpression networks, which outperforms traditional statistical tests at identifying stress-related genes. Analysis of an Arabidopsis stress expression data set led to the prediction of candidate stress-related genes showing expression and network changes in response to multiple abiotic stresses. Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning–based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. The mlDNA first used a ML-based filtering process to remove nonexpressed, constitutively expressed, or non-stress-responsive “noninformative” genes prior to network construction, through learning the patterns of 32 expression characteristics of known stress-related genes. The retained “informative” genes were subsequently analyzed by ML-based network comparison to predict candidate stress-related genes showing expression and network differences between control and stress networks, based on 33 network topological characteristics. Comparative evaluation of the network-centric and gene-centric analytic methods showed that mlDNA substantially outperformed traditional statistical testing–based differential expression analysis at identifying stress-related genes, with markedly improved prediction accuracy. To experimentally validate the mlDNA predictions, we selected 89 candidates out of the 1784 predicted salt stress–related genes with available SALK T-DNA mutagenesis lines for phenotypic screening and identified two previously unreported genes, mutants of which showed salt-sensitive phenotypes.
Health sequelae of human cryptosporidiosis in immunocompetent patients.

BACKGROUND There have been no systematic studies following up the longer term health effects of cases of cryptosporidiosis for which genotype data exist. METHODS We report a follow-up study of cases of laboratory-confirmed cryptosporidiosis. Case patients were sent a postal questionnaire asking about a wide range of symptoms occurring within 2 months after their initial diagnosis, and control subjects were sent the questionnaire 2 months after they had been recruited to the original study. RESULTS Completed questionnaires were received from 235 case patients and 232 control subjects. For 111 of the case patients, the species of the infecting strain was known; 61 of these strains were Cryptosporidium hominis (human genotype), and 50 were Cryptosporidium parvum (bovine genotype). Forty percent of the case patients reported recurrence of intestinal symptoms after resolution of the acute stage of illness, irrespective of whether infection was with C. hominis or C. parvum. Reports of joint pain (odds ratio [OR], 2.8), eye pains (OR, 2.44), recurrent headache (OR, 2.10), dizzy spells (OR, 1.69), and fatigue (OR, 3.0) were significantly more common in case patients than in control subjects, but only in people who had experienced C. hominis infection. Joint symptoms experienced by case patients were of longer duration than those experienced by control subjects. CONCLUSIONS Our results confirm previous reports of a high rate of relapse of gastrointestinal symptoms following recovery from an acute episode of cryptosporidiosis and show that C. hominis but not C. parvum is associated with an increased risk of nonintestinal sequelae. This study demonstrates that the impact of cryptosporidiosis on public health extends beyond that of the acute diarrheal illness and can lead to significant health sequelae.
AgileQube: An approach for specification and detection of agile smells

This paper presents the thesis entitled “AgileQube: an approach for specification and detection of agile smells” (Telemaco 2020 [24]) submitted to COPPE/UFRJ as part of the requirements for obtaining the degree of Doctor of Science (D.Sc.). In the thesis, we aimed to contribute to the area of agility assessment (which is an investigation on how a company or a team is adopting agile practices) in the following way: first, we investigated existing agility assessment approaches and identified the following problems: To address these problems, we extended the code smell term to the context of agility assessment, introduced the agile smell metaphor to denote a situation that may harm the adoption of an agile practice and proposed an agility assessment approach that automatically (or semi-automatically) detects agile smells in agile projects. The thesis produced the following contributions: To validate the solution, we conducted 2 case studies that aimed at detecting agile smells in agile projects. The resulting contributions addressed the problems identified in the existing agility assessment approaches and the reports generated in the case studies confirmed that the proposed approach, along with the other contributions, was able to automatically detect agile smells in the assessed agile projects.
Spectrally opponent inputs to the human luminance pathway: slow +M and −L cone inputs revealed by intense long‐wavelength adaptation

The nature of the inputs to achromatic luminance flicker perception was explored psychophysically by measuring middle‐ (M‐) and long‐wavelength‐sensitive (L‐) cone modulation sensitivities, M‐ and L‐cone phase delays, and spectral sensitivities as a function of temporal frequency. Under intense long‐wavelength adaptation, the existence of multiple luminance inputs was revealed by substantial frequency‐dependent changes in all three types of measure. Fast (f) and slow (s) M‐cone input signals of the same polarity (+sM and +fM) sum at low frequencies, but then destructively interfere near 16 Hz because of the delay between them. In contrast, fast and slow L‐cone input signals of opposite polarity (−sL and +fL) cancel at low frequencies, but then constructively interfere near 16 Hz. Although these slow, spectrally opponent luminance inputs (+sM and −sL) would usually be characterized as chromatic, and the fast, non‐opponent inputs (+fM and +fL) as achromatic, both contribute to flicker photometric nulls without producing visible colour variation. Although its output produces an achromatic percept, the luminance channel has slow, spectrally opponent inputs in addition to the expected non‐opponent ones. Consequently, it is not possible in general to silence this channel with pairs of ‘equiluminant’ alternating stimuli, since stimuli equated for the non‐opponent luminance mechanism (+fM and +fL) may still generate spectrally opponent signals (+sM and +sL).
Advantages of using microfabricated extracellular electrodes for in vitro neuronal recording

We describe fabrication methods and the characterisation and use of extracellalar microelectrode arrays for the detection of action potentials from neurons in culture. The 100 μm2 platinised gold microelectrodes in the 64 electrode array detect the external current which flows during an action potential with S:N ratios of up to 500:1, giving a maximum recorded signal of several millivolts. The performance of these electrodes is enhanced if good sealing of the cells over the electrodes is obtained and further enhanced if the electrodes and the cells lie in a deep groove in the substratum. The electrodes can be used for both recording and stimulation of activity in cultured neurons and for recording from multiple sites on a single cell. The use of such electrodes to obtain recordings from invertebrate neurons is described. The particular advantages of these electrodes, their long term stability, non‐invasive nature, high packing density, and utility in stimulation, are demonstrated. © 1995 Wiley‐Liss, Inc.
IL-32, a novel cytokine with a possible role in disease

IL-32 is the name given to the NK4 transcript first reported in IL-2 activated T lymphocytes and natural killer cells 13 years ago without known function. The novel cytokine has six isoforms. In an study to isolate a soluble form of the IL-32 receptor from human urine, IL-32α bound proteinase-3 with high affinity and was not affected by enzyme inhibition. IL-32α/IL-32γ were expressed as recombinant molecules. The cytokine exhibits properties characteristic of proinflammatory cytokines and also induces the degradation of inhibitory κB and phosphorylation of mitogen activated protein p38. Monoclonal antibodies to IL-32 identify its presence in a variety of human tissues from diseases states. Epithelial cells from healthy subjects express low levels of the cytokine, but in disease conditions such as chronic obstructive pulmonary disease, Crohn’s disease and psoriasis, the expression increases markedly. IL-32 is a major transcript in gene array studies in epithelial cells stimulated with IFNγ in vitro. In rheumatoid arthritis, synovial tissues reveals increased content of IL-32, which correlates with severity of disease. A highly significant correlation has been observed between the number of synovial and macrophagic cells positive for IL-32 and the level of erythrocytes sedimentation, IL-1β, tumour necrosis factor α, and IL-18. Thus, IL-32 exhibits many properties of proinflammatory cytokines and associations with disease severity.
Real time location system using passive UHF RFID

RFID technology is becoming more and more popular these days and on its top stands passive UHF RFID technology for it's economical as well as practical benefits. Even though this technology is intended for inventory, several attempts have been made by several vendors in creating a real-time location tracking system using passive RFID solutions. The scope of this paper is description of experiments when developing such a RTLS with 9 RFID readers spread into a rectangular grid at the area of 64 to 100 meters square. Each reader connected to 4 antennas facing specified direction. Location algorithm combines signal strength values with number of reads to obtain tags location probability. Experiments with this settings were run in October and November 2013 at the Southern Alberta Institute of Technology, Calgary, Canada in cooperation with Dean Brennan of the RFID Application Development (RAD) Lab Team and visiting professor from Technical University of Liberec, Czech Republic (Jan Kolaja). The most interesting result of these space consuming experiments is self-calibrating algorithm. Although the system has not been sufficiently finished yet as it is limited by having not enough powerful antennas, the experiments have earned many beneficial knowledge.
Dose‐dependent systemic and renal haemodynamic effects of angiotensin II in conscious lambs: role of angiotensin AT1 and AT2 receptors

The present experiments were designed to measure the effects of acute administration of angiotensin (ANG) II on mean arterial pressure (MAP) and renal blood flow (RBF) in conscious, chronically instrumented lambs at two different stages of postnatal maturation, and to determine the receptors through which these effects of ANG II are elicited. Experiments consisted of haemodynamic measurements for 10 s before (Control) and for 60 s after intravenous (i.v.) administration of one of 11 doses of ANG II (0–200 ng kg−1). Administration of ANG II was associated with a dose‐dependent increase in MAP to a maximal effective concentration (EC100) of 100 ng kg−1 in lambs aged 1 and 6 weeks. Administration of ANG II has caused a dose‐dependent decrease in RBF, with EC100 values of 50 ng kg−1 in 1‐week‐old lambs, and 25 ng kg−1 in 6‐week‐old lambs. Responses to ANG II at the EC50 were also measured in the presence of the specific ANG II AT1 receptor antagonist, ZD 7155, the specific AT2 receptor antagonist, PD 123319, and vehicle. Administration of ZD 7155, but not PD 123319 or vehicle, abolished the MAP and RBF responses to ANG II in both age groups. In addition, MAP decreased and RBF increased in both age groups after administration of ZD 7155, but not PD 123319; the effects were similar in both age groups. These data provide new information that pressor and renal vasoconstrictor effects of ANG II during the first 6 weeks of postnatal life in lambs are elicited by activation of AT1 but not AT2 receptors.
A study of the pharmacologic treatment of medication-compliant schizophrenics who relapse.

BACKGROUND Maintenance antipsychotic medications greatly diminish the risk of relapse in schizophrenic patients. A significant number, however, will relapse despite ongoing drug treatment. This is a report of a pilot study of a group of schizophrenic patients who relapsed despite having been compliant with treatment. METHOD The authors studied 32 schizophrenic patients who had been compliant with pharmacologic treatment but who had suffered a relapse and were admitted to the hospital. Maintained on their usual pharmacologic treatment, they also received in a double-blind fashion either fluphenazine or placebo. Clinical assessments were done on Day 1 and Day 10. RESULTS The authors found no effect of additional neuroleptic treatment on outcome. Two-thirds of the subjects showed at least moderate improvement during the study. Subjects who were experiencing greater severity of depression on admission were more likely to improve. There was no association between baseline ratings of psychosis and outcome. CONCLUSION This study offers preliminary evidence that increasing the dose of neuroleptic does not improve outcome in schizophrenics who have relapsed while taking antipsychotic medications. Most of these patients will improve during the course of a brief hospitalization.