Miracle-dz/UniFAR-FTUs huggingface dataset:
The six-minute stepper test is related to muscle strength but cannot substitute for the one repetition maximum to prescribe strength training in patients with COPD

Purpose: There are many barriers to pulmonary rehabilitation, including a limited access to evaluation centers. To cope with these difficulties, field tests are often used to prescribe endurance training. As field tests are related to muscle strength, they could also be used to prescribe strength training and increase the access to pulmonary rehabilitation in rural area. However, their validity for this purpose has never been studied. Patients and methods: The relationship between the 6-minute stepper test (6MST), 6-minute walk test, maximal workload achieved during cardiopulmonary exercise testing (Wpeak), and one repetition maximum (1RM) was assessed in 35 patients with COPD through a retrospective chart review to derive predictive equation of the 1RM from these tests. The effectiveness of these equations to prescribe strength training at 70% of the 1RM was assessed in an independent cross-validation group of 34 patients with COPD. Results: There was a moderate relationship between the 6MST, Wpeak and the 1RM ( r = 0.44 and r = 0.41, respectively, both P # 0.01). Whatever the test, the prescription of strength training using the estimated 1RM compared with the measured 1RM resulted in a mean absolute difference and a mean bias of about 30 kg. Conclusion: The use of the 6MST and Wpeak for the prescription of strength training would result in a clinically not acceptable error. Therefore, they should not be used as a substitute for the 1RM to prescribe strength training.
Activities of Daily Living and Life-Space Mobility in Older Adults with Chronic Obstructive Pulmonary Disease

Purpose The aim of this study was to investigate whether limitation during the performance of activities of daily living (ADL) was associated with life-space mobility in older people with chronic obstructive pulmonary disease (COPD), and to generate a regression model for life-space mobility score. Patients and Methods This cross-sectional study with a convenience sample included older people (aged ≥60 years old) with COPD. We assessed participants’ lung function (spirometry), life-space mobility (University of Alabama at Birmingham Study of Aging Life-Space Assessment questionnaire), severity of dyspnea (Modified Dyspnea Index) and limitation during the performance of ADL (London Chest Activity of Daily Living). We used Pearson’s correlation to investigate the associations between the measures, and multiple linear regression to detect which of the measures influenced life-space mobility. Statistical significance was set at 5%. Results Fifty participants completed all the assessments (29 females [58%]; mean ± SD age of 67 ± 6 years old, FEV1 47 ± 29% of predicted, and body mass index 22.5 ± 11.6 kg/m2). Their mean scores for life-space mobility and for limitation during the performance of ADL were 49.7 ± 27.2 and 16.46 ± 9.74, respectively. We found a strong inverse correlation between limitation during the performance of ADL and life-space mobility (r = −0.57, p = <0.01) as well as between severity of dyspnea and life-space mobility (r= 0.86, p= <0.01). Both sex and limitation during the performance of ADL were considered as independent factors associated to life-space mobility (R2= 0.56). Conclusion In this study, limitations during the performance of ADL and dyspnea had a strong correlation with life-space mobility in older adults with COPD. Also, alongside sex, the limitation during the performance of ADL is an independent factor associated with life-space mobility in a regression model.
A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition

Abstract 4,6-Diamino-5-formamidopyrimidine (Fapy•dG) is an abundant form of oxidative DNA damage that is mutagenic and contributes to the pathogenesis of human disease. When Fapy•dG is in its nucleotide triphosphate form, Fapy•dGTP, it is inefficiently cleansed from the nucleotide pool by the responsible enzyme in Escherichia coli MutT and its mammalian homolog MTH1. Therefore, under oxidative stress conditions, Fapy•dGTP could become a pro-mutagenic substrate for insertion into the genome by DNA polymerases. Here, we evaluated insertion kinetics and high-resolution ternary complex crystal structures of a configurationally stable Fapy•dGTP analog, β-C-Fapy•dGTP, with DNA polymerase β. The crystallographic snapshots and kinetic data indicate that binding of β-C-Fapy•dGTP impedes enzyme closure, thus hindering insertion. The structures reveal that an active site residue, Asp276, positions β-C-Fapy•dGTP so that it distorts the geometry of critical catalytic atoms. Removal of this guardian side chain permits enzyme closure and increases the efficiency of β-C-Fapy•dG insertion opposite dC. These results highlight the stringent requirements necessary to achieve a closed DNA polymerase active site poised for efficient nucleotide incorporation and illustrate how DNA polymerase β has evolved to hinder Fapy•dGTP insertion.
Distinct generation of subjective vividness and confidence during naturalistic memory retrieval in the angular gyrus

Subjective experience of remembering is a hallmark of episodic memory, which is deemed crucial for effective behavior. A fundamental and enduring puzzle is the origin of confidence in memory; for example, does the confidence during episodic retrieval depend upon the subjective sensed vividness? The angular gyrus (AnG) exhibits a sensitivity to the subjective experience of remembering, but its direct contribution to the monitoring of subjective mnemonic experience has hitherto been lacking. Here, using a naturalistic video-watching paradigm combined with repetitive transcranial magnetic stimulation (rTMS) and resting-state functional magnetic resonance imaging, we found that pre-retrieval rTMS targeting the left AnG selectively alters the vividness efficiency compared to control stimulation while keeping metacognitive efficiency and objective memory accuracy unaffected. Using trial-wise data, we showed that AnG stimulation altered the mediating role of vividness in confidence in the accuracy of memory judgment. Furthermore, resting-state functional connectivity of hippocampus and AnG was specifically associated with vividness efficiency, while the connectivity of hippocampus and medial prefrontal cortex was associated with metacognitive efficiency across individuals. These findings identify the causal involvement of AnG in gauging the vividness, but not the confidence, of memory, thereby providing evidence for a differentiation account of conscious assessment of memory retrieval.
Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain ∆6

ABSTRACT Bacillus subtilis ∆6 is a genome-reduced strain that was cured from six prophages and AT-rich islands. This strain is of great interest for biotechnological applications. Here, we announce the full-genome sequence of this strain. Interestingly, the conjugative element ICEBs1 has most likely undergone self-excision in B. subtilis ∆6.
Impacts and Attitudes of Posture on Daily Function, Disability, and Psychological Measures in College Students

Background: College students engage in large amounts of sedentary behavior which have been linked to adverse mental health outcomes. Poor postural habits due to the increase in this behavior, in conjunction with prolonged mobile phone usage, can lead to poor posture in these younger populations. As such, this study aims to identify how college-students feel about their posture, the prevalence of pain patterns, psychological status, and their knowledge of intervention options available. Methods: A descriptive, observation survey study collected data from a healthy college-age population of 58 male and 100 female (n = 158) (mean = 21.6 ± 1.9y). Survey included assessments of self-perceived attitudes regarding posture, ergonomics, neck disability (NDI), mental health outcomes, knowledge of postural rehabilitation techniques, and range of motion (ROM). Results: In total, 88.6% of participants wished their posture was better, 93.7% and 96.2% believed their standing and sitting postures could be improved, respectively. Thirty-five percent of participants qualified as Mild or Moderate Disability based upon their cumulative NDI scores. Strong correlations (r = 0.61) between participants' self-reported need to improve standing and sitting posture, and a moderate correlation (r = -0.47) between pain when sitting and total NDI. Conclusion: We noted a prevalence of posture-related issues and the impacts on daily function including sleeping and sitting. Future research should look to objectively assess posture through validated measures to investigate the extent of posture-related pain and dysfunction. To alleviate early-onset neck pain and reduce the risk of developing future chronic neck pain, college aged populations need education on proper posture and rehabilitation interventions designed to alleviate pain and dysfunction over the short-and long-term.
A NEW APPROACH FOR CLASSIFICATION OF ATHEROSCLEROSIS OF COMMON CAROTID ARTERY FROM ULTRASOUND IMAGES

Background and objectives: The diagnosis of carotid atherosclerosis is of vital importance, as this cardiovascular disease may cause myocardial infarction. One-third of deaths in the world occur due to myocardial infarction, commonly known as heart attack. Atherosclerosis is deposition of plaque in artery wall. It could be detected from the features of intima-media complex of the artery wall. This study proposes a new classification approach to distinguish between symptomatic and asymptomatic plaques using non-invasive carotid B-mode ultrasound images. These two types of plaques have diverse impacts on human life. In the first condition, slowly plaque formation reaches life-threatening condition and the second condition is acute in nature. Hence treatment protocol is to be decided based on the type of plaque. Methods: To locate the intima-media-complex region, the images are segmented using snake-based segmentation algorithm. Several features are extracted using fixed size blocks selected from the segmented region using gray-level co-occurrence matrix. Finally classification is performed using support vector machine. Results: The performance shows improvement in accuracy using lesser number of features than previous works. The reduction in feature size is achieved by incorporating segmentation in the pre-processing stage. In the classifier, 10-fold cross-validation protocol is used for training and testing and an accuracy of 100% is obtained. Conclusion: This proposed technique could work as an adjunct tool in quick decision-making for cardiologists and radiologists.
Integral Projection Models and analysis of patch dynamics of the reef building coral Monstastraea annularis

Over the past 40 years, coral cover has reduced by as much as 80%. At the same time, Coral Reefs are coming under increasing threat from hurricanes, as climate change is expected to increase the intensity of hurricanes. Therefore, it has become increasingly important to understand the effect of hurricanes on a coral population. This Thesis focuses on the reef-building coral Montastraea annularis. This species once dominated Caribbean Coral Reefs, but is fast being replaced by faster growing more opportunistic species. It is important that the underlying dynamics of the decline is understood, if managers stand any chance of reversing this decline. The aim of this Thesis is to investigate the effect of hurricane activity on the dynamics of the reef-building coralMontastraea annularis. To achieve this the Integral Projection Model (IPM) method was adopted and the results compared to those produced using the more traditional method of Population Projection Matrix (PPM) method. The models were fitted using census data from June 1998 to January 2003, which described the area of individual coral patches on a sample of ramets on Glovers Reef, Belize. Glovers Reef is a marine reserve that lies 30km off the coast of Belize and 15km east of the main barrier reef. Three hurricanes struck Glovers Reef during the study: Hurricane Mitch (October 1998), Hurricane Keith (September 2000) and Hurricane Iris (October 2001). The data have been divided by two different methods in order to test two research questions, firstly if the initial trauma following a hurricane affects the long term dynamics of a population and, secondly, if the dynamics exhibited during a hurricane varied with hurricane strength. In this Thesis five main results are shown: 1. All models for all divisions of data are in long term decline. 2. As initial trauma increased, the long term growth rates decreased, conversely the short term extremes increased. 3. Fragmentation is more likely as patch size increased and more likely under stronger hurricanes. 4. Integral Projection Modelling painted a similar picture to Population Projection Matrix models and should be a preferred method of analysis.
Modelling durations of multiple spells from longitudinal survey data

We investigate some modifications of the classical single­spell Cox model in order to handle multiple spells from the same individual when the data are collected in a longitudinal survey based on a complex sample design. One modification is the use of a design­based approach for the estimation of the model coefficients and their variances; in the variance estimation each individual is treated as a cluster of spells, bringing an extra stage of clustering into the survey design. Other modifications to the model allow a flexible specification of the baseline hazard to account for possibly differential dependence of hazard on the order and duration of successive spells, and also allow for differential effects of the covariates on the spells of different orders. These approaches are illustrated using data from the Canadian Survey of Labour and Income Dynamics (SLID).
Type I γ phosphatidylinositol phosphate kinase is required for EGF-stimulated directional cell migration

Phosphatidylinositol 4,5-bisphosphate (PI4,5P2) has been implicated in many biological processes, including vesicular traffi cking (Downes et al., 2005), secretion (Martin, 2001), focal adhesion and cytoskeleton assembly (Ling et al., 2006), regulation of ion channels (Delmas et al., 2005), and nuclear signaling pathways (Gonzales and Anderson, 2006). PI4,5P2 has a role not only as a substrate of PLC and phosphoinositol 3-kinase–mediated second messenger production, but also as a direct effector that binds to and regulates the function of many PI4,5P2-interacting proteins (Anderson and Marchesi, 1985; Heck et al., 2007). The generation of PI4,5P2 in cells primarily occurs through the phosphorylation of phosphatidylinositol(4) phosphate (PI[4]P) by type I phosphatidylinositol phosphate kinases (PIPKI; Doughman et al., 2003a). Three isoforms of PIPKI (Iα, Iβ, and Iγ) have been characterized along with several splice variants. By associating with their unique binding partners, different PIPKI isoforms produce PI4,5P2 with distinct subcellular distributions, from which they perform individual biological functions (Anderson et al., 1999; Coppolino et al., 2002; Doughman et al., 2003b; Heck et al., 2007). Cell migration requires the coordination of many biochemical events, including organized adhesion formation and turnover as well as dynamic cytoskeletal rearrangements (Horwitz and Parsons, 1999; Webb et al., 2002). PI4,5P2 binds to and regulates many proteins that are crucial for the assembly of the migratory machinery. For example, PI4,5P2 regulates reorganization of the actin cytoskeleton by associating with α-actinin, WASP/ N-WASP, gelsolin, cofi lin, profi lin, and villin (Niggli, 2005; Ling et al., 2006). PI4,5P2 has also been proposed to regulate adhesions by binding to and modulating talin, vinculin, ezrin/ radixin/moesin, calpain, and other proteins involved in adhesion dynamics (Niggli, 2005; Ling et al., 2006). PI4,5P2 is therefore positioned to play key roles in migration by modulating adhesion dynamics and cytoskeleton rearrangement. Many observations indicate that PI4,5P2 is a key signaling molecule in the regulation of cell migration, yet the role of specifi c PIP kinases in the regulation of cell migration remains to be clarifi ed. PIPKIγ is alternatively spliced in cells, resulting in at least two major variants, PIPKIγ635 and PIPKIγ661, which differ by a 26-amino-acid C-terminal extension (Ishihara et al., 1998). Most interesting, the 26-amino-acid C-terminal extension binds to talin and targets PIPKIγ661, but not PIPKIγ635, to adhesions (Di Paolo et al., 2002; Ling et al., 2002). This specifi c Type Iγ phosphatidylinositol phosphate kinase is required for EGF-stimulated directional cell migration
Collision Resistance of Double-Block-Length Hash Function against Free-Start Attack

In this article, we discuss the security of double-block-length (DBL) hash functions against the free-start collision attack. We focus on the DBL hash functions composed of compression functions of the form F(x) = (f(x), f(p(x))), where f is a smaller compression function and p is a permutation. We first show, in the random oracle model, that a significantly good upper bound can be obtained on the success probability of the free-start collision attack with sufficient conditions on p and the set of initial values. We also show that a similar upper bound can be obtained in the ideal cipher model if f is composed of a block cipher.
LANE OCCUPATION MODELS IN MOTORWAY SECTIONS BEFORE A TOLL-GATE STATION

The paper analyses lane occupation in some three lane motorway sections preceding a toll-gate station. Using data collected on a Northern Italian motorway over a period of about nine months and by treating them appropriately the distribution of flow over the three lanes for four sections is studied. This distribution depends on the three fundamental variables, speed, flow and density, but also on composition of flow (percentage of heavy vehicles), environmental variables (brightness and visibility) and on which section is considered (near or far a toll-gate).
SHAPING SMART HOME PRODUCT SERVICE SYSTEM (SH-PSS) REFLECTION CRITERIA CARDS FOR ‘TILES IOT INVENTOR TOOLKIT’

The rapid growth of the Internet of Things (IoT) has provided new opportunities for the development of Smart Home Product-Service Systems (SH-PSS) as technological solutions to various problems. However, designers face challenges in generating ideas for such systems. This study aims to address this challenge by developing an extended Tiles IoT Inventor toolkit specifically designed for SH-PSS design. The toolkit utilizes a card-based approach to identify consumer problems and explore the technical capabilities of SH-PSS during the ideation process. To assess its effectiveness, the IoT Ideation toolkit was evaluated through workshops involving user experience designers, product designers, and human-computer interaction (HCI) students. Additionally, this study identifies five attractive characteristics of SH-PSS that influence technology adoption and introduces SH-PSS Reflection Criteria Cards as part of the Tiles IoT Inventor Toolkit. Research questions are formulated to investigate the enhancement of idea generation ability, service dominance and the identification of technology adoption discontinuities using these reflection criteria cards. Hypotheses are proposed and will be tested through experiments involving control and experimental groups. This study contributes significantly to design education, providing valuable support for design practitioners and researchers in identifying consumer problems and exploring the technical capabilities of SH-PSS.
Fecal Microbiota Transplantation in Human Immunodeficiency Virus-Infected Patient Population: A Systematic Review and Meta-Analysis

Background Patients with human immunodeficiency virus (HIV) infection suffer from alterations in gut microbiota due to recurrent gastrointestinal infections and systemic inflammation. Fecal microbiota transplantation (FMT) appears to be a potential therapy; however, there are concerns about its safety. Likewise, no previous meta-analysis evaluated FMT efficacy in HIV-infected patients. Methods We conducted a thorough electronic search on PubMed, Scopus, OVID, Web of Science, and Cochrane CENTRAL for clinical studies assessing the safety and efficacy of FMT in patients with HIV and gastrointestinal dysbiosis, where FMT was indicated to restore the disrupted microbiota. Results FMT significantly restored the typical microbiome in patients with Clostridium difficile (C. difficile) and non-C. difficile and reduced the risk of gastrointestinal infections in HIV patients receiving antiretroviral therapy (odds ratio (OR) = 0.774, 95% confidence interval (CI): (0.62, 0.966)). Furthermore, adverse events, such as distention and bloating, associated with FMT were comparable between HIV and health controls (OR = 0.60, 95% CI: (0.07, 4.6)), with no statistical difference. Conclusions Current evidence demonstrated that FMT is safe and effective in HIV patients suffering from alterations in gut microbiota. We recommend further multi-centric clinical studies to address the optimal transplant amount and source for FMT. To the best of our knowledge, this is the first meta-analysis to assess the safety and efficacy of FMT in patients with HIV.
LONG-RUN DETERMINANTS OF ATMOSPHERIC CO 2: GRANGER-CAUSALITY AND COINTEGRATION ANALYSIS

Atmospheric concentrations of CO 2 grew annually 1.12 + 0.48 parts per million (ppm) in 1958- 1984, and 1.72 + 0.54 ppm (mean + standard deviation) in 1985-2009, so that the rate growth is growing itself. Natural phenomena that influence short-run changes in CO 2 atmospheric levels (through their influence on CO 2 emissions and sinks) are stationary processes that cannot explain the growth of CO 2 levels at an increasing rate. Cointegration tests show at a high level of statistical significance that the annual increase of CO 2 concentrations is roughly proportional to "human activities" as measured by the money value of the world economy and the size of the world population. We find that population and world GDP help to predict CO 2 concentrations, but CO 2 concentrations do not help to predict the other variables; that is, there is Ganger causality from population and world economic output to CO 2. Though the smallness of the time series involved and the theoretical and practical issues posed by cointegration allow only for a limited confidence in these results, they have obvious major implications. For business-as- usual conditions and a world economy growing annually 3.5%—the mean annual growth of the world economy since 1960—the required world population to maintain or reduce CO 2 levels would be 1.3 billion or less. For a world population of 7 billion as the present one, CO 2 atmospheric levels would decrease if the global economy contracted annually 24.5% or more.
Physics of Neutron Star Crusts

The physics of neutron star crusts is vast, involving many different research fields, from nuclear and condensed matter physics to general relativity. This review summarizes the progress, which has been achieved over the last few years, in modeling neutron star crusts, both at the microscopic and macroscopic levels. The confrontation of these theoretical models with observations is also briefly discussed.