Miracle-dz/UniFAR-FTUs huggingface dataset:
The process of decline in advanced activities of daily living: a qualitative explorative study in mild cognitive impairment

ABSTRACT Background: The notion of “minimal impairment in instrumental activities of daily living (i-ADL)” is important in the diagnosis of mild cognitive impairment (MCI), but is presently not adequately operationalized. ADL is stratified according to difficulty, complexity, and also to vulnerability to early cognitive changes in a threefold hierarchy: basic activities of daily living (b-ADL), i-ADL, and advanced activities of daily living (a-ADL). This study aims to gain a deeper understanding of the functional decline in the process of MCI. Methods: In a qualitative design, 37 consecutive patients diagnosed with amnestic (a)-MCI and their proxies were interviewed at two geriatric day hospitals. Constant comparative analysis was used for the analysis. Results: The a-ADL-concept emerged as important in the diagnosis of MCI. All participants were engaged in a wide range of activities, which could be clustered according to the International Classification of Functioning, Disability and Health (ICF). Participants reported subtle difficulties in performance. A process of functional decline was identified in which adaptation and coping mechanisms interacted with the process of reduced skills, leading to an activity disruption and an insufficiency in functioning. Conclusion: This study asserts the inclusion of an evaluation of a-ADL in the assessment of older persons. When evaluating ADL at three levels (b-ADL, i-ADL, and a-ADL), all the activities one can perform in daily living are covered.
Evaluation of real time polymerase chain reaction assays for confirmation of Neisseria gonorrhoeae in clinical samples tested positive in the Roche Cobas Amplicor assay

Objective: Development of a rapid, sensitive, and accurate assay for confirmation of Neisseria gonorrhoeae in clinical samples. Method: Two real time polymerase chain reaction (PCR) assays, developed on the LightCycler for amplification of the N gonorrhoeae cppB gene, were utilised for confirmation of this bacterial pathogen in samples positive by the Roche Cobas Amplicor assay. Performance characteristics of the two assays were compared with other commercial nucleic acid amplification assays, including the Abbott LCx and Roche 16S rRNA tests. Results: All related Neisseria as well as other bacterial species tested negative by both cppB gene based assays, whereas 120 N gonorrhoeae clinical isolates from various geographical regions gave in positive results. Both assays had a sensitivity of one copy per reaction. 122 clinical samples positive and another 50 samples negative for N gonorrhoeae by Roche Cobas Amplicor were selected from a specimen pool of more than 3000 women tested previously. Overall, 73 of 122 (59.8%) samples were confirmed as positive. The two real time assays had sensitivities of 99% and 100% and specificities of 98% and 100%, respectively. The 16S and LCx assays produced similar results to the real time assays, indicating a similar sensitivity to and specificity of both real time assays. Conclusion: The data from this study highlight the need to confirm N gonorrhoeae positive Cobas Amplicor PCR results as an important part of the testing algorithm of all diagnostic laboratories utilising this assay.
Effect of dietary α -tocopherol concentration on performance and some immune responses in broiler chickens fed on diets containing oils from different sources

1. An investigation was carried out into the effects of dietary α-tocopherol (α-T) concentration and source of supplemental oil on performance, activity of anti-oxidative enzymes and some immune responses in broilers from day-old to 41 d of age. 2. Three dietary concentrations of α-T (10, 50 and 100 mg/kg) with three sources of supplemental oil (sunflower - SFO, palm - PMO and safflower - SAO) were provided using a 3 × 3 experimental design. 3. Body weight gain and food conversion efficiency were not affected by either interaction or concentrations of α-T and sources of oil in diet. 4. Concentrations of total protein, globulin, triglycerides and cholesterol in sera increased significantly with dietary α-T concentration irrespective of the source of oil. Significantly higher concentration of serum albumin was evident in broilers fed on the SFO-based diet and the concentration of globulin was higher in groups fed on those diets containing PMO and SAO. 5. The lipid peroxidation (LP), measured as MDA release, decreased with the concentration of α-T in a dose-related manner with SFO- and SAO-based diets, although not with the PMO-based diet. With different oil sources, LP was significantly lower with the PMO-based diet compared to the others. Activities of glutathione peroxidase and RBC catalase increased and heterophil: lymphocyte ratio was reduced with concentration of α-T for each source of oil tested. 6. Assays for humoral and cell-mediated immune responses indicated no effect of the source of dietary supplemental oil or interaction, although an increasing concentration of dietary α-T improved cell-mediated immune responses. 7. It is concluded that sunflower oil, palm oil and safflower oil can be used as sources of oil for broiler diets without having any effect on performance, immune responses or the activity of anti-oxidizing enzymes. Higher concentrations of dietary α-tocopherol (50 or 100 mg/kg) reduced lipid peroxidation activity and enhanced activities of anti-oxidative enzymes, they also improved the cell-mediated immune responses in commercial broilers.
How Do Physicians Provide Statistical Information about Antidepressants to Hypothetical Patients?

Background. Little is known about how physicians provide statistical information to patients, which is important for informed consent. Methods. In a survey, obstetricians and gynecologists (N = 142) received statistical information about the benefit and side effects of an antidepressant. They received information in various formats, including event rates (antidepressant v. placebo), absolute risks, and relative risks. Participants had to imagine 2 hypothetical patients, 1 for whom they believed the drug to be safe and effective and 1 for whom they did not, and select the information they would give those patients. We assessed whether the information they selected for each patient was complete, transparent, interpretable, or persuasive (i.e., to nudge patients toward a particular option) and compared physicians who gave both patients the same information with those who gave both patients different information. Results. A similar proportion of physicians (roughly 25% each) selected information that was 1) complete and transparent, 2) complete but not transparent, 3) not interpretable for the patient because necessary comparative information was missing, or 4) suited for nudging. Physicians who gave both patients the same information (61% of physicians) more often selected at least complete information, even if it was often not transparent. Physicians who gave both patients different information (39% of physicians), in contrast, more often selected information that was suited for nudging in line with the belief they were asked to imagine. A limitation is that scenarios were hypothetical. Conclusions. Most physicians did not provide complete and transparent information. Clinicians who presented consistent information to different patients tended to present complete information, whereas those who varied what information they chose to present appeared more prone to nudging.
Prevalence and Predictors of Chronic Health Conditions of Inmates Newly Admitted to Maximum Security Prisons

This study estimated the prevalence of chronic medical conditions and risk predictors of 759 newly admitted inmates in two New York State maximum-security prisons. The most prevalent conditions were respiratory (34.1%), cardiovascular (17.4%), and sexually transmitted diseases (STD; 16.1%); least prevalent were HIV (3.6%), cancer (1.7%), and kidney disease (1.7%). Results of the multivariable logistic regression showed that females had higher risk for all conditions except cardiovascular and liver disease; individuals aged 40 years and older had significantly higher risk for all conditions except asthma and STD; non-Hispanic Black inmates had higher risk for respiratory disease and STD; cigarette smoking was associated with asthma; and obesity was significantly associated with diabetes, asthma, and cardiovascular conditions. These findings highlight the heavy burden of chronic illnesses among newly admitted inmates and the need to address adequate screening, prevention, and treatment services.
AN ILLUSTRATION OF MULTILEVEL MODELS FOR ORDINAL RESPONSE DATA

In C. Reading (Ed.), Data and context in statistics education: Towards an evidence-based society. Proceedings of the Eighth International Conference on Teaching Statistics (ICOTS8, July, 2010), Ljubljana, Slovenia. Voorburg, The Netherlands: International Statistical Institute. www.stat.auckland.ac. nz/~iase/publications.php [© 2010 ISI/IASE] AN ILLUSTRATION OF MULTILEVEL MODELS FOR ORDINAL RESPONSE DATA
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

Motivation: As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. Results: We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE, and as interest grows in long non-coding RNAs, often initially recognized by their lack of protein coding potential rather than conserved RNA secondary structures. Availability and Implementation: The Objective Caml source code and executables for GNU/Linux and Mac OS X are freely available at http://compbio.mit.edu/PhyloCSF Contact: mlin@mit.edu; manoli@mit.edu
Relationship between intra‐ and postoperative oxygen transport and prolonged intensive care after cardiac surgery: a prospective study

Background: Prolonged intensive care is a rare but serious complication of cardiac surgery. It is required in less than 10% of operated patients but they use more than 30% of all the intensive care resources needed for cardiac surgery. The aim of our study was to describe the clinical course of the patients who need prolonged intensive care following cardiac surgery and to assess whether the intra‐ and postoperative oxygen transport variables are different in these patients as compared to patients with an uncomplicated course.
Buccal cell DNA yield, quality, and collection costs: comparison of methods for large-scale studies.

There is considerable interest in noninvasive and cost-effective methods for obtaining DNA in large-scale studies. In this randomized crossover study of 22 participants, we compared the DNA yield, quality, and associated costs of buccal cell DNA collected using cytobrushes (three brushes per collection) and swish (i.e., mouthwash) in self-administered procedures. There was a nonstatistically significant higher yield from the mouthwash compared with cytobrush collections (15.8 microg versus 12.0 microg, respectively; P = 0.53). PCR reactions that required short (0.3 kb) or intermediate (1.1 kb) DNA fragments were 100% successful for DNA from brush and mouthwash, whereas PCRs for reactions that required long fragments (7.8 kb) failed for all of the participants from cytobrush DNA and were 81% successful for DNA from the mouthwash source. The brush collections provided sufficient DNA for an estimated 150-225 PCR reactions requiring short and intermediate DNA fragments. The estimated per person costs for buccal brush DNA collections in large studies were less then half (8.50 dollars) those for the mouthwash method (18 dollars). In addition, we tested whether cytobrush instructions to rub cheeks before collection or collect cells only in the morning increased DNA yield and whether repeat brushings of the same cheek reduced DNA yield. These variations resulted in no significant differences in DNA yields. We conclude that the collection of DNA with cytobrushes using simple instructions is cost effective in large-scale studies, and yields sufficient quantity and quality of DNA for genotyping.
Laser-Generated Shockwaves for the Disruption of Bacterial Biofilms

The goal of this thesis was to explore the use of laser-generated shockwaves as a potential methodology to treat bacterial infected surfaces as they are a major burden on the healthcare industry. A modified version of the Laser Spallation Technique (LST) was built to measure the intrinsic adhesion strength of S. epidermidis biofilms (RP62A) grown on polystyrene surfaces. Previously, the LST was used to successfully measure the adhesion strengths of mammalian cells. The system is based on a Q-switched, Nd:YAG pulsed laser with an output wavelength of 1,064 nm and a pulse width between 2-6 ns that ablates titanium-coated soda-lime glass slides (under confinement), thereby causing unipolar compressive waves. The modified LST successfully measured the adhesion strength of S. epidermidis biofilms grown on polystyrene, under static growth conditions, to be 22.75+/-0.16%. High strain rates of 1.544x10^5 s^-1 and 1.41x10^6 s^-1 in glass and in biofilm, respectively, were calculated, and total strains of 0.3% in glass and 3% in the S. epidermidis biofilm are reported and are below published failure strains. Current techniques that measure biofilm material properties vary significantly due to viscoelastic effects of biofilms under lower strain rates. Due to the high strain rates and only purely compressive/tensile loading, the adhesive failure in the biofilm is an intrinsic strength measurement.With motivation to use these glass modified shockwaves on infected wounds, studies were implemented to evaluate the effect of the shockwaves on porcine samples ex vivo. Due to the impedance mismatch of the glass slides with the coupling medium (water), a compressive train of shockwaves are created. Peak stresses varying from 21-266.5 MPa of the shockwave, with subsequent stress pulses with 18% less peak stress, reached the pigskin surface and caused no qualitative structural damage. This is a very important result as other studies have used similar stress profiles, as a single shockwave, to deliver drugs through the skin and biofilm structures.Finally, a low-cost, high-speed imaging system was developed and characterized to capture shockwave-induced phenomenon, i.e. cavitation. Unlike other techniques including extracorporeal shockwave (ESW) therapy, which has a tensile component in the stress profile and thus causing cavitation-induced damage in biological structures, laser-generated shockwaves are purely compressive and will only have tensile components at interfaces, depending on the impedance of each layer. Cavitation bubbles were successfully imaged at the glass/water interface which propagated toward the biofilm and caused localized delaminations.
A Functional Genomic Screen Combined with Time-Lapse Microscopy Uncovers a Novel Set of Genes Involved in Dorsal Closure of Drosophila Embryos

Morphogenesis, the establishment of the animal body, requires the coordinated rearrangement of cells and tissues regulated by a very strictly-determined genetic program. Dorsal closure of the epithelium in the Drosophila melanogaster embryo is one of the best models for such a complex morphogenetic event. To explore the genetic regulation of dorsal closure, we carried out a large-scale RNA interference-based screen in combination with in vivo time-lapse microscopy and identified several genes essential for the closure or affecting its dynamics. One of the novel dorsal closure genes, the small GTPase activator pebble (pbl), was selected for detailed analysis. We show that pbl regulates actin accumulation and protrusion dynamics in the leading edge of the migrating epithelial cells. In addition, pbl affects dorsal closure dynamics by regulating head involution, a morphogenetic process mechanically coupled with dorsal closure. Finally, we provide evidence that pbl is involved in closure of the adult thorax, suggesting its general requirement in epithelial closure processes.
A Review of Methods to Detect Cases of Severely Malnourished Children in the Community for Their Admission into Community-Based Therapeutic Care Programs

Background The complexity and cost of measuring weight-for-height make it unsuitable for use by community-based volunteers. This has led community therapeutic care programs to adopt a two-stage screening and admission procedure in which mid-upper-arm circumference (MUAC) is used for referral and weight-for-height is used for admission. Such a procedure results in many individuals being referred for care on the basis of MUAC but subsequently being refused treatment because they do not meet the weight-for-height admission criterion. This “problem of rejected referrals” has proved to be a major barrier to program uptake. Objective To systematically review methods to detect cases of severely malnourished children in the community for their admission into community-based therapeutic care programs. Methods Clinical and anthropometric methods for case detection of severely malnourished children in the community were reviewed with regard to their ability to reflect both mortality risk and nutritional status. Results MUAC, with the addition of the presence of bipedal edema, was found to be the indicator best suited to screening and case detection of malnutrition in the community. The case definition “MUAC < 110 mm OR the presence of bipedal edema,” with MUAC measured by a color-banded strap, is suitable for screening and case detection of malnutrition in the community for children aged between 6 and 59 months. Monitoring and discharge criteria were also reviewed. Conclusions There is no compelling evidence to support a move away from using weight in combination with clinical criteria for monitoring and discharge.
R-Tree Index Optimization

The optimization of spatial indexing is an increasingly important issue considering the fact that spatial databases, in such diverse areas as geographical, CAD/CAM and image applications, are growing rapidly in size and often contain on the order of millions of items or more. This necessitates the storage of the index on disk, which has the potential of slowing down the access time signi cantly. In this paper, we discuss ways of minimizing the disk access frequency by grouping together data items which are close to one another in the spatial domain (\packing"). The data structure which we seek to optimize here is the R-tree for a given set of data objects. Existing methods of building an R-tree index based on spacelling curves (Peano, Hilbert) are computationally cheap, but they do not preserve spatial locality well, in particular when dealing with higher-dimensional data of non-zero extent. On the other hand, existing methods of packing based on all dimensions of the data, such as the several proposed dynamic R-tree insertion algorithms, do not take advantage of the fact that all the data objects are known beforehand. Furthermore, they are essentially serial in nature. In this paper, we regard packing as an optimization problem and propose an iterative method of nding a close-to-optimal solution to the packing of a given set of spatial objects in D dimensions. The method achieves a high degree of parallelism by constructing the R-tree bottom-up. In experiments on data of various dimensionalities and distributions, we have found that the proposed method can signi cantly improve on the packing performance of the R* insertion algorithm and the Hilbert curve. It is shown that the improvements increase with the skewness of the data and, in some cases, can even amount to an order of magnitude in terms of decreased response time.
Designing Neural Network Architectures using Reinforcement Learning

At present, designing convolutional neural network (CNN) architectures requires both human expertise and labor. New architectures are handcrafted by careful experimentation or modified from a handful of existing networks. We introduce MetaQNN, a meta-modeling algorithm based on reinforcement learning to automatically generate high-performing CNN architectures for a given learning task. The learning agent is trained to sequentially choose CNN layers using $Q$-learning with an $\epsilon$-greedy exploration strategy and experience replay. The agent explores a large but finite space of possible architectures and iteratively discovers designs with improved performance on the learning task. On image classification benchmarks, the agent-designed networks (consisting of only standard convolution, pooling, and fully-connected layers) beat existing networks designed with the same layer types and are competitive against the state-of-the-art methods that use more complex layer types. We also outperform existing meta-modeling approaches for network design on image classification tasks.
Raman spectroscopy of murine bone in response to simulated spaceflight conditions

Astronauts exposed to spaceflight conditions can lose 1-2% of their bone mineral density per month from the weight-bearing portions of the skeletal system. Low bone mineral density, termed osteopenia, is the result of decreased bone formation and/or increased bone resorption. In this study, Raman spectroscopy is used to examine if the physicochemical composition of murine femurs is altered in response to simulated spaceflight conditions (hindlimb suspension). Female C57BL/6J mice, aged 53 days, were divided into ground control and simulated spaceflight groups for a period of 12 days, modeling the experiment profile of mice flown on Space Shuttle flight STS-108. After the study, the mice were sacrificed and femur specimens harvested. Mid-diaphysis sections were probed using near-infrared Raman microscopy. Spectra were collected at various anatomical sites (anterior, lateral, medial, and posterior quadrants) and/or cortical locations (periosteal, midosteal, and endosteal). Chemometric recovery of spectra was employed to reduce signal contributions from the epoxy embedding agent. Mean values for mineralization, carbonation, crystallinity, and other parameters associated with the matrix were estimated. Correlations between mineralization and carbonation were observed, despite the small absolute changes between the two groups. We present more detailed analysis of this data and comment on the prospects for Raman spectroscopic evaluation of bone quality in hindlimb suspended (HLS) specimens.