Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular epidemiology of HIV in Ghana: Dominance of CRF02_AG

Recent studies showed the importance of CRF02_AG in West Africa, although the clinical relevance of these recombinant forms of HIV remains unknown. The present study aimed at determining the molecular diversity of HIV in Ghana and investigating the possible epidemiologic advantage of recombinant HIV‐1. Plasma samples collected in 1999–2002 from two populations of HIV infected individuals (144 asymptomatic candidate blood donors and 169 AIDS patients) were studied and 249 of them were molecularly characterised in gag, pol, and env regions. Five molecular groups were identified: strains clustering with CRF02_AG in all regions (147/249 or 59%), recombinant strains clustering with CRF02_AG in one or two regions (50/249 or 20%), other subtypes, pure or recombinant, but not involving CRF02_AG (37/249 or 15%), HIV‐2 (11/249 or 4.5%), and double infections (4/249 or 1.5%). There was no significant difference in the distribution of HIV‐1 recombinant strains according to clinical presentation. No evidence of a significant increase in CRF02_AG prevalence between 1999 and 2002 was found. Irrespective of clinical condition, CRF02_AG is the predominant molecular form of HIV‐1 in Kumasi, Ghana. J. Med. Virol. 73:158–166, 2004. © 2004 Wiley‐Liss, Inc.
Hemispheric Asymmetry in Accessing Word Meanings: Concrete and Abstract Nouns

The present experiments investigated hemispheric differences in the brain in accessing concrete and abstract word meanings. For this purpose, an automatic semantic priming paradigm was used with a short stimulus onset asynchrony between prime and target (250 msec.) as well as a low proportion of related trials. (20%). Analysis showed that for concrete nouns, priming effects were observed in both hemispheres. There was greater priming in the right hemisphere, suggesting hemispheric differences in accessing semantic representations of concrete nouns. For abstract nouns, on the other hand, priming patterns in the right hemisphere were identical to those in the left hemisphere, suggesting that information about abstract nouns projected to the right hemisphere may be transferred to the dominant left hemisphere for further processing.
Z-DNA crystallography .

We review the effect of sequence on the structure of left-handed Z-DNA in single crystals. The various substituent groups that define a nucleotide base as guanine, cytosine,thymine, or adenine affect both the DNA conformation and the organization of solvent around the duplex. These are discussed in terms of their effect on the ability of sequences to adopt the unusual Z-DNA structure. In addition, the experimental and theoretical methods used to treat DNA hydration are discussed as they relate to the stability of Z-DNA . Finally, we argue that Z-DNA , as defined by the crystal conformation, is sufficient in itself to account for the physical properties of left-handed conformations observed in polymers and in genomic sequences
Black Beetle Virus: Messenger for Protein B Is a Subgenomic Viral RNA

Black beetle virus induces the synthesis of three new proteins, protein A (molecular weight, 104,000), protein α (molecular weight, 47,000), and protein B (molecular weight, 10,000), in infected Drosophila cells. Two of these proteins, A and α, are known to be encoded by black beetle virus RNAs 1 and 2, respectively, extracted from virions. We found that RNA extracted from infected cells directed the synthesis of all three proteins when it was added to a cell-free protein-synthesizing system. When polysomal RNA was fractionated on a sucrose density gradient, the messengers for proteins A and α cosedimented with viral RNAs 1 (22S) and 2 (15S), respectively. However, the messenger for protein B was a 9S RNA (RNA 3) not found in purified virions. Like the synthesis of viral RNAs 1 and 2, intracellular synthesis of RNA 3 was not affected by the drug actinomycin D at concentrations which blocked synthesis of host cell RNA. This indicated that RNA 3 is a virus-specific subgenomic RNA and, therefore, that protein B is a virus-encoded protein.
Health Utilities for Children and Adults With Type 1 Diabetes

ObjectiveWe studied health utilities in patients with type 1 diabetes to understand potential differences in health utilities as function of age, type of respondent (self report vs. proxy report), and method of assessment (direct vs. indirect). Research Design and MethodsWe elicited self-reported health utilities for adults (n=213) and children (n=238) with type 1 diabetes, and by parent proxy report (n=223) for overall quality of life [Health Utilities Index (HUI) Mark 3 and experienced time-trade-off (TTO) questions] and hypothetical complication states (TTO questions). ResultsMean health utilities for overall quality of life (QOL) ranged from 0.81 to 0.91. Children had significantly higher overall QOL compared with adults (0.89 vs. 0.85, P<0.01) by HUI, but had no significant difference in QOL by TTO. There were no significant differences in QOL between child self report and parent proxy report. Utilities were higher for HUI versus TTO for parent proxy report (P<0.01) but not for adult or child self report. Utilities for hypothetical complication states were lower than for current QOL. Values were lower for stroke (0.34 to 0.53), end stage renal disease (0.47 to 0.55), and blindness (0.52 to 0.69) than for amputation (0.73 to 0.82) and angina (0.74 to 0.80). Complication utilities for parent proxy report were higher compared with adult self report for most hypothetical complication states. ConclusionsIndividuals with type 1 diabetes with few complications report a relatively high QOL; however, future end stage complications are rated as having a significant impact on QOL. Differences in utilities by age, self report versus proxy report, and method raise important questions about whose utilities should be used in economic analyses.
Non-metallic ultrasound probe holder for co-collection and co-registration with EMA

Co-collection and co-registration of ultrasound images of the tongue and articulometry data requires the stabilization of the ultrasound probe relative to the head using a non-metallic system. Audio, ultrasound, and articulometry data were recorded from 11 North American English speakers reading 10 blocks of 25 sentences, speaking for 2 minutes at a time, spanning a recording time of 45 minutes. The 95% confidence interval for ultrasound probe roll relative to head motion was 1.35◦, and 2.12 mm for lateral displacement, such that ultrasound probe displacement is within acceptable rotational and translational parameters as described in the HOCUS paper [9]. The proper use of this probe holder could also allow for adequate ultrasound probe stabilization without external marker tracking for post-processing correction, making this probe holder suitable for field research.
Cutting Edge: Cytotoxic Granule Polarization and Cytolysis Can Occur without Central Supramolecular Activation Cluster Formation in CD8+ Effector T Cells1

The functional implication of molecular segregation within the immunological synapse remains uncertain. We recently reported that effector but not naive TCR transgenic murine CD8+ T cells formed immunological synapses containing a central supramolecular activation cluster (cSMAC), suggesting that execution of effector functions such as cytolytic activity might be facilitated by the cSMAC structure. We have now explored this hypothesis using two approaches. First, by simultaneously imaging cSMAC formation and mobilization of cytotoxic granules to the synapse, we observed no correlation between the presence of a cSMAC and granule reorientation. Second, we took advantage of the observation that CD28 costimulation markedly enhances cSMAC formation. Granule polarization to the contact site was indistinguishable with B7-1+ and B7-1− target cells, and cytolytic activity against B7-1+ or B7-1− targets was similar and granule-dependent. Together, our results indicate that the formation of a cSMAC is not required for cytolytic activity in CD8+ effector T cells.
Explosive Radiation or Cryptic Mass Extinction? Interpreting Signatures in Molecular Phylogenies

How biodiversity is generated and maintained underlies many major questions in evolutionary biology, particularly relating to the tempo and pattern of diversification through time. Molecular phytogenies and new analytical methods provide additional tools to help interpret evolutionary processes. Evolutionary rates in lineages sometimes appear punctuated, and such “explosive” radiations are commonly interpreted as adaptive, leading to causative key innovations being sought. Here we argue that an alternative process might explain apparently rapid radiations (“broom-and-handle” or “stemmy” patterns seen in many phytogenies) with no need to invoke dramatic increase in the rate of diversification. We use simulations to show that mass extinction events can produce the same phylogenetic pattern as that currently being interpreted as due to an adaptive radiation. By comparing simulated and empirical phytogenies of Australian and southern African legumes, we find evidence for coincident mass extinctions in multiple lineages that could have resulted from global climate change at the end of the Eocene.
Feature Control as Intrinsic Motivation for Hierarchical Reinforcement Learning

One of the main concerns of deep reinforcement learning (DRL) is the data inefficiency problem, which stems both from an inability to fully utilize data acquired and from naive exploration strategies. In order to alleviate these problems, we propose a DRL algorithm that aims to improve data efficiency via both the utilization of unrewarded experiences and the exploration strategy by combining ideas from unsupervised auxiliary tasks, intrinsic motivation, and hierarchical reinforcement learning (HRL). Our method is based on a simple HRL architecture with a metacontroller and a subcontroller. The subcontroller is intrinsically motivated by the metacontroller to learn to control aspects of the environment, with the intention of giving the agent: 1) a neural representation that is generically useful for tasks that involve manipulation of the environment and 2) the ability to explore the environment in a temporally extended manner through the control of the metacontroller. In this way, we reinterpret the notion of pixel- and feature-control auxiliary tasks as reusable skills that can be learned via an intrinsic reward. We evaluate our method on a number of Atari 2600 games. We found that it outperforms the baseline in several environments and significantly improves performance in one of the hardest games—Montezuma’s revenge—for which the ability to utilize sparse data is key. We found that the inclusion of intrinsic reward is crucial for the improvement in the performance and that most of the benefit seems to be derived from the representations learned during training.
Thyroid Cytopathology with an Emphasis on the ‘Atypical Cells of Uncertain Significance' Category: A 3-Year Audit with Cytohistologic Correlation

Background: The National Cancer Institute meeting of 2007 resulted in the reporting terminology for thyroid cytopathology. The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) aims to standardise thyroid cytopathology reporting for cytology centres and clinicians alike. Study Objective: To compare our laboratory's performance against TBSRTC. The second aim was to determine our laboratory's atypia of undetermined significance/follicular cells of undetermined significance (AUS/FLUS) reporting rate and malignant outcomes. Our laboratory subclassifies the AUS/FLUS category into AUS/FLUS not otherwise specified (NOS) and AUS/FLUS cannot exclude malignancy. Materials: All thyroid reports were retrieved from our computerised database for the period of January 1, 2008 to March 31, 2011. Histologic correlation was obtained where available, and cases were classified according to their original diagnosis into 1 of the 6 categories of TBSRTC. Results: A total of 1,767 cases were retrieved. The categories were as follows: inadequate (n = 415; 23%), benign (n = 1,063; 60%), AUS/FLUS (n = 141; 8%) [NOS (n = 93; 5%) and cannot exclude malignancy (n = 48; 3%)] suspicious for follicular/Hürthle cell neoplasm (n = 68; 4%), suspicious for malignancy (n = 37; 2%) and malignant (n = 43; 2%). The malignant rates for the categories were as follows: -6 (26%), 0 (0%), 8 (40%), 9 (38%), 11 (42%), 15 (62.5%), and 15 (94%), respectively. Conclusion: We have shown that the AUS category carries a higher malignant rate than that of the AUS category in TBSRTC of 5-15%. We conclude that subclassifying the AUS/FLUS category into NOS and cannot exclude malignancy helps to better identify patients with an increased risk of malignancy in the AUS/FLUS cannot exclude malignancy category.
Study of morbidity of personnel with potential exposure to vinclozolin.

OBJECTIVES--To examine internal exposure and targeted health outcomes of employees exposed to 3-(3,5-dichlorophenyl)-5-methyl-5-vinyl-1,3-oxazolidine-2,4-dione; chemical abstracts service (CAS) number: 50471-44-8 (vinclozolin). METHODS--A cross sectional study of 67 men exposed to vinclozolin for one to 13 years during synthesis and formulation operations and 52 controls. Biomonitoring was based on determination of urinary metabolites that contained a 3,5-dichloroaniline (3,5-DCA) moiety. Targeted health endpoints were the same as in previous subchronic and chronic animal studies--namely, reversible changes in the concentrations of hormones of the adrenocorticotrophic and gonadotrophic feedback systems, signs of liver injury, haemolytic anaemia, cataract formation (uniquely in rats), and hormonally induced hyperplasia and tumours at high doses. The clinical investigation consisted of a medical and occupational history questionnaire, physical examination, laboratory determinations (including testosterone, LH, and FSH measurements), ultrasonography of the liver and prostate, a detailed eye examination, and routine spirometry. RESULTS--The mean 3,5-DCA concentration for two thirds of the study group exceeded an equivalent of the vinclozolin acceptable daily intake (ADI) used for consumer regulatory purposes. Even the highest concentrations were, however, at least 10 times below the no observable adverse effect level (NOAEL) based on animal studies. Analysis of physical examination and laboratory data provided no evidence of hormonal responses induced by vinclozolin. Furthermore, no evidence of liver injury, prostate changes, cataract formation, or haemolytic anaemia was found. CONCLUSION--There was no evidence of any health effects induced by vinclozolin among employees with potential long term exposure. In particular, no antiandrogenic effects were found.
Failure of Protein to Protect Against Cholesterol Atherogenesis in Underfed Rabbits

Summary 1. Study of effect of protein on development of experimental atherosclerosis on blood lipids and lipoproteins, in underfed rabbits with supplementary cholesterol, was performed. 2. Cholesterol fed rabbits on a limited intake of standard laboratory food lost approximately one-fourth of their body weight. A marked degree of atherosclerosis, increased blood lipids and lipoproteins was produced. 3. Cholesterol-fed rabbits on a limited intake of a relatively high protein diet, who lost equivalent amounts of weight, developed approximately the same degree of atherosclerosis, increase in blood lipids and lipoproteins.
Direct Ertapenem Disk Screening Method for Identification of KPC-Producing Klebsiella pneumoniae and Escherichia coli in Surveillance Swab Specimens

ABSTRACT Klebsiella pneumoniae carbapenemase (KPC) production in Gram-negative bacilli is an increasing problem worldwide. Rectal swab surveillance is recommended as a component of infection prevention programs, yet few screening methods are published. We compared detection of KPC-producing Klebsiella pneumoniae and Escherichia coli in surveillance specimens by 2 methods: (i) inoculation of swabs in tryptic soy broth containing 2 μg/ml imipenem followed by plating to MacConkey agar (MAC) (method 1) and (ii) streaking swabs on MAC onto which a 10-μg ertapenem disk was then placed (method 2). Simulated rectal swab specimens of challenge isolates from a collection of well-characterized K. pneumoniae and E. coli strains and salvage rectal swab specimens collected from patients at 4 different health care facilities over a 7-month period were tested. The gold-standard comparator was bla KPC PCR testing of isolates. Method 1 detected 4/9 (44%) KPC-positive challenge isolates. By method 2, 9/9 KPC-positive challenge isolates exhibited zones of inhibition of ≤27 mm; all KPC-negative isolates exhibited zones of inhibition greater than 27 mm. The sensitivity and specificity of method 1 for detection of KPC-positive K. pneumoniae and E. coli in 149 rectal swab specimens were 65.6% (95% confidence interval [CI], 46.8% to 80.8%) and 49.6% (95% CI, 40.3% to 58.9%), respectively. With method 2, a zone diameter of ≤27 mm had a sensitivity of 97.0% (95% CI, 82.5% to 99.8%) and specificity of 90.5% (95% CI, 83.3% to 94.9%) for detection of KPC in rectal swab specimens. Direct ertapenem disk testing is simpler, more sensitive, and more specific than selective broth enrichment with imipenem for detection of KPC-producing K. pneumoniae and E. coli in surveillance specimens.
Identification of plasmid-mediated quinolone resistance genes qnrA1, qnrB1 and aac(6')-1b-cr in a multiple drug-resistant isolate of Klebsiella pneumoniae from Chennai.

PURPOSE Resistance to fluoroquinolones, a commonly prescribed antimicrobial for Gram-negative and Gram-positive microorganisms, is of importance in therapy. The purpose of this study was to screen for the presence of Plasmid-Mediated Quinolone Resistance (PMQR) determinants in clinical isolates of Klebsiella pneumoniae. MATERIALS AND METHODS Extended-Spectrum Beta-Lactamase (ESBL) isolates of K. pneumoniae collected during October 2009 were screened by the antimicrobial susceptibility test. The plasmids from these isolates were analysed by specific Polymerase chain Reaction (PCR) for qnrA, qnrB and aac(6')-1b. The amplified products were sequenced to confirm the allele. RESULTS Our analysis showed that 61% out of the 23 ESBL K. pneumoniae isolates were resistant to ciprofloxacin and 56% to levofloxacin. The PMQR was demonstrated by transforming the plasmids from two isolates P12 and P13 into E. coli JM109. The PMQR gene qnrA was found in 16 isolates and qnrB in 11 isolates. The plasmid pKNMGR13 which conferred an minimum inhibitory concentration (MIC) of more than 240 μg/ml in sensitive E. coli was found to harbour the qnrA1 and qnrB1 allele. Furthermore, the gene aac(6')-1b-cr encoding a variant aminoglycoside 6'-N Acetyl transferase which confers resistance to fluoroquinolones was found in the same plasmid. CONCLUSIONS Our report shows the prevalence of PMQR mediated by qnrA and qnrB in multidrug-resistant K. pneumoniae isolates from Chennai. A multidrug-resistant plasmid conferring high resistance to ciprofloxacin was found to harbour another PMQR gene, aac(6')-1b-cr mutant gene. This is the first report screening for PMQR in K. pneumoniae isolates from India.
Failing Bodies: Body Image and Multiple Chronic Conditions in Later Life

There is a rich qualitative tradition of examining the lived experience of singular chronic conditions as well as the relationship between illness and identity in chronic disease. There has been little exploration of the experience of multiple chronic conditions or how these health issues may influence body image in later life. Building on the extant research and providing an alternative lens for understanding the experience of health issues, this article examines the body images of older adults with five or more chronic conditions. We use data from in-depth interviews with 10 men and 10 women aged 68 to 88 to analyze how older adults perceive their bodies to be failing in terms of their appearances, functional abilities, and impending mortality. We discuss how the participants view their bodies as both aesthetic and instrumental entities and how gender norms and discourses of successful aging and healthism shape their body evaluations.
The incidence of auditory and vestibular concussion following minor head injury

HEAD injury is one of the most common causes of neurological disorder in this modern technological age. There were 142,000 admissions to hospitals in 1972, and probably another 70,000 consulted their general practitioners. Jennet (1975) suggests that 4-5 times as many attend Accident Departments but are not admitted. Remarkably little is known about the development of auditory and vestibular disturbance due to such injuries and less is known about the incidence of otoneurological disorders following such injuries despite their relative importance both medically and legally. The aim of this investigation is to examine the incidence of otoneurological abnormalities in the immediate post-injury period in patients with minor head injuries (without evidence of direct involvement of ears) admitted through a busy Accident Department and to try to determine whether there is a risk factor necessitating a more comprehensive assessment of their audio-vestibular function. Deafness is a known sequel to head injury. Mawson (1967) states, however, that deafness is unlikely if the injury is not severe enough to cause concussion. Its incidence is not certain and the prognosis is even more uncertain. Conventional teaching suggests that if deafness* is present for one month then recovery is prognostically poor; if longer, the chances of recovery are negligible. Vertigo forms part of the post-concussional syndrome and is reputed to be more prevalent in patients claiming compensation. It is also reputed that the dizziness following head injury is a disturbance in the autonomic control of vasomotor tone. 'Post-concussional syndrome' is the name given to a group of symptoms following head injury comprising headache, giddiness, poor concentration and poor memory with possibly emotional disturbance. Its aetiology is uncertain and whether it is psychogenic or organic is still a matter of debate. Lewin (1970) argues that the concept needs to be abandoned and suggests that each symptom has a different aetiology and needs separate assessment and treatment. It is against a background of such inconclusive evidence that an attempt is also made to try to determine whether a particular type of injury occurring at a particular site producing a particular otoneurological disturbance has a more favourable or less favourable
A Geostatistical Approach to Large‐Scale Disease Mapping with Temporal Misalignment

Summary Temporal boundary misalignment occurs when area boundaries shift across time (e.g., census tract boundaries change at each census year), complicating the modeling of temporal trends across space. Large area‐level datasets with temporal boundary misalignment are becoming increasingly common in practice. The few existing approaches for temporally misaligned data do not account for correlation in spatial random effects over time. To overcome issues associated with temporal misalignment, we construct a geostatistical model for aggregate count data by assuming that an underlying continuous risk surface induces spatial correlation between areas. We implement the model within the framework of a generalized linear mixed model using radial basis splines. Using this approach, boundary misalignment becomes a nonissue. Additionally, this disease‐mapping framework facilitates fast, easy model fitting by using a penalized quasilikelihood approximation to maximum likelihood estimation. We anticipate that the method will also be useful for large disease‐mapping datasets for which fully Bayesian approaches are infeasible. We apply our method to assess socioeconomic trends in breast cancer incidence in Los Angeles between the periods 1988–1992 and 1998–2002.