Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics

In plants, an oligogene family encodes NADP-malic enzymes (NADP-me), which are responsible for various functions and exhibit different kinetics and expression patterns. In particular, a chloroplast isoform of NADP-me plays a key role in one of the three biochemical subtypes of C4 photosynthesis, an adaptation to warm environments that evolved several times independently during angiosperm diversification. By combining genomic and phylogenetic approaches, this study aimed at identifying the molecular mechanisms linked to the recurrent evolutions of C4-specific NADP-me in grasses (Poaceae). Genes encoding NADP-me (nadpme) were retrieved from genomes of model grasses and isolated from a large sample of C3 and C4 grasses. Genomic and phylogenetic analyses showed that 1) the grass nadpme gene family is composed of four main lineages, one of which is expressed in plastids (nadpme-IV), 2) C4-specific NADP-me evolved at least five times independently from nadpme-IV, and 3) some codons driven by positive selection underwent parallel changes during the multiple C4 origins. The C4 NADP-me being expressed in chloroplasts probably constrained its recurrent evolutions from the only plastid nadpme lineage and this common starting point limited the number of evolutionary paths toward a C4 optimized enzyme, resulting in genetic convergence. In light of the history of nadpme genes, an evolutionary scenario of the C4 phenotype using NADP-me is discussed.
Ceramide selectively inhibits early events in the response of human neutrophils to tumor necrosis factor

Cell spreading and the respiratory burst of neutrophils responding to soluble, physiological agents and adherent to model biological surfaces are typically delayed in onset by 15 min or more. The lag period may be a physiologically important feature of the action of such agents on neutrophils in that it may allow for migration before secretion. However, the mechanism that interposes such a long delay between stimulus and response is unknown. Tumor necrosis factor α (TNF‐α) mediates some of its actions by triggering sphingomyelinase to generate ceramide. In adherent human neutrophils, however, exogenous ceramide did not mimic TNF‐α's ability to stimulate cell spreading, paxillin tyrosine phosphorylation, or the respiratory burst. On the contrary, ceramide suppressed each such response. Ceramide did so by extending the lag period in the cells' response to TNF‐α. Ceramide extended the lag period whether it was added exogenously or generated endogenously by sphingomyelinase, and the effect was reversible. Remarkably, however, ceramide inhibited cell spreading or the respiratory burst only if added together with TNF‐α or within the next few minutes. Neutrophils ignored ceramide if it was added later, even if the TNF‐α‐triggered respiratory burst had not yet commenced. These features suggest that an early, brief elevation of ceramide in response to TNF‐α could mediate the lag period. By temporarily inhibiting tyrosine phosphorylation, cell spreading, and the respiratory burst, ceramide or a functionally similar mediator could serve as a phase coordinator of the neutrophil's response to soluble agonists.
Re-engineering female friendly science

Introduction - Female Friendly Science Goes Mainstream Curriculum Integration - Transformation or Assimilation? Consequences of Ignoring Gender and Race in Group Work Fruitful Dialogues - What Single-Sex and Coeducational Institutions Can Tell Each Other About Women and Science Gender Equity in the School to Work Environment - Reinforcement of Race, Class and Gender Stereotypes Feminist Critiques of Science as Usual Applying Feminist Theories to Women and Science Programmes Evaluating Female Friendly Interventions Dangerous Times - Threats to Female Friendly Science Posed by the New Right and Tight Fiscal Resources.
Supercontinuum generation in tapered fibers.

Supercontinuum light with a spectrum more than two octaves broad (370-1545 nm at the 20-dB level) was generated in a standard telecommunications fiber by femtosecond pulses from an unamplified Ti:sapphire laser. The fiber had been tapered to a diameter of :2mum over a 90-mm length. The pulse energy was 3.9 nJ (average power, 300 mW). This source of high-intensity single-mode white light should find widespread applications in frequency metrology and spectroscopy, especially since no unconventional fibers are needed.
Using Spatial Manipulation to Examine Interactions between Visual and Auditory Encoding of Pitch and Time

Music notations use both symbolic and spatial representation systems. Novice musicians do not have the training to associate symbolic information with musical identities, such as chords or rhythmic and melodic patterns. They provide an opportunity to explore the mechanisms underpinning multimodal learning when spatial encoding strategies of feature dimensions might be expected to dominate. In this study, we applied a range of transformations (such as time reversal) to short melodies and rhythms and asked novice musicians to identify them with or without the aid of notation. Performance using a purely spatial (graphic) notation was contrasted with the more symbolic, traditional western notation over a series of weekly sessions. The results showed learning effects for both notation types, but performance improved more for graphic notation. This points to greater compatibility of auditory and visual neural codes for novice musicians when using spatial notation, suggesting that pitch and time may be spatially encoded in multimodal associative memory. The findings also point to new strategies for training novice musicians.
Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore

Aims: We undertook this study to define the incidence of toxigenic Clostridium difficile in our hospital and to characterise the isolates. Methods: All unformed stool was tested for the presence of Toxin A (TcdA) and Toxin B (TcdB), and cultured for C. difficile. Culture filtrates were also tested for TcdA and TcdB. Detection of tcdA and tcdB genes was carried out for A−B+ strains by polymerase chain reaction (PCR). The minimum inhibitory concentrations (MICs) of metronidazole, vancomycin and clindamycin for all isolates were tested using the Etest. PCR ribotyping was carried out on all isolates. Results: The incidence of Clostridium difficile associated disease (CDAD) was 3.2 cases per 1000 admissions or discharges and 53.8 cases per 100 000 patient days. Most cases occurred in renal and haematology patients. CDAD was more common in patients aged over 50 years and of male gender. The Indian population was under‐represented. Fourteen (11.8%) isolates were A−B+. All strains were susceptible to metronidazole but one strain showed intermediate resistance to vancomycin. Only 12.8% of the isolates were susceptible to clindamycin. Thirty‐five isolates had PCR ribotype A, of which 29 (83%) had a clindamycin MIC >256 mg/L. Thirty‐three had PCR ribotype B, of which only one (3%) had a clindamycin MIC >256 mg/L. The 14 A−B+ strains were all PCR ribotype C, and had a range of MICs for clindamycin from 2 to >256 mg/L. Conclusions: The incidence of CDAD in our hospital is relatively low. Isolates remain susceptible to metronidazole and vancomycin.
Nested Markov Properties for Acyclic Directed Mixed Graphs

Directed acyclic graph (DAG) models may be characterized in four different ways: via a factorization, the d-separation criterion, the moralization criterion, and the local Markov property. As pointed out by Robins [2, 1], Verma and Pearl [6], and Tian and Pearl [5], marginals of DAG models also imply equality constraints that are not conditional independences. The well-known 'Verma constraint' is an example. Constraints of this type were used for testing edges [3], and an efficient variable elimination scheme [4]. Using acyclic directed mixed graphs (ADMGs) we provide a graphical characterization of the constraints given in [5] via a nested Markov property that uses a 'fixing' transformation on graphs. We give four characterizations of our nested model that are analogous to those given for DAGs. We show that marginal distributions of DAG models obey this property.
Child Maltreatment and Psychological Distress Among Urban Homeless Youth

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Calculation of protein and energy requirements in beluga sturgeon (Huso huso) using a factorial approach.

This study tried to determine the protein and energy requirements of growing beluga sturgeon Huso huso using a factorial approach. The experiment was composed of four small-scale growth trails covering different weight ranges. The fish fed at 0, 20, 40, 60, 80 and 100% of satiation. DWG had a steady increase throughout the experiment following a non-linear equation as Y = 1.433 (±0.056) × Ln(X) -2.740 (±0.261); r(2) = 0.99, p < 0.001, where Y = weight gain (g/day) and X = fish weight (g). The daily requirement of digestible energy (DE) for maintenance amounted to 79.09 kJ × BW (kg)(0.8) . The daily requirement of DP for maintenance calculated as 0.93 g × BW (kg)(0.7) . The relationship between DE intake (X) and DE gain (Y) expressed as Y = -0.0004 (±0.000) X(2) + 0.600 (±0.082) X -44.95 (± 6.72). Also, the relationship between DP intake (X) and protein gain (Y) was expressed as Y = -0.019 (±0.006) X(2) + 0.548 (±0.062) X - 0.498 (±0.121). The daily requirements of energy and protein were estimated as 79.09 kJ × BW (kg)(0.8) + 2.94 × DE gain and 0.93 g × BW (kg)(0.7) + 2.63 × DP gain. Apparently, beluga sturgeon is inefficient in converting energy and protein into body tissue. Therefore, energy content of the diet should be sufficiently high to satisfy large energy demands in beluga sturgeon and also to reduce the catabolism of protein.
Type of Bone Graft or Substitute Does Not Affect Outcome of Spine Fusion With Instrumentation for Adolescent Idiopathic Scoliosis

Study Design. Retrospective cohort analysis. Objective. To compare clinical outcomes after spine instrumentation and fusion using 3 different bone grafts in children with adolescent idiopathic scoliosis (AIS). Summary of Background Data. Autogenous iliac crest bone graft (AIC) is the “gold standard” to promote fusion in posterior AIS operations, although the morbidity of harvest is a concern. There is limited data comparing outcomes after AIS surgery based on types of bone grafts. Methods. Children (10–18 yr) with AIS who underwent deformity correction via a posterior approach were identified in the Spinal Deformity Study Group database. All had a minimum of 2-year follow-up. Patients were subdivided into 3 groups based on bone graft used: AIC, allograft, and bone substitute (BS). Clinical data included patient demographics, operative details, postoperative analgesic use, and perioperative complications. Lenke curve type and curve magnitude changes were radiographically analyzed. The Scoliosis Research Society-30 questionnaire was used to assess clinical outcomes. Results. 461 patients met inclusion criteria (girls: 381, boys: 80; average age 14.7 ± 1.7) and consisted of 152 AIC patients (124 girls, 28 boys), 199 allograft patients (167 girls, 32 boys), and 110 BS patients (90 girls, 20 boys). There was no difference in age (P = 0.41) or gender (P = 0.82). The BS group had significantly smaller preoperative curves and shorter operative times. Postoperatively, patients who received BS had significantly longer hospital stays, used higher quantities of patient-controlled intravenous analgesia and used epidurals longer. The AIC group used patient-controlled intravenous analgesia significantly longer. There were no differences between the groups in regards to curve type, number of levels fused, postoperative infections, pseudarthrosis, reoperations for any indication, and Scoliosis Research Society-30 scores at the latest follow-up. Conclusion. Outcomes after primary posterior spinal fusion with instrumentation are not influenced by type of bone graft or substitute. Level of Evidence: 3
Ageing, the Urban-Rural Gap and Disability Trends: 19 Years of Experience in China - 1987 to 2006

Background As the age of a population increases, so too does the rate of disability. In addition, disability is likely to be more common in rural compared with urban areas. The present study aimed to examine the influence of rapid population changes in terms of age and rural/urban residence on the prevalence of disability. Methods Data from the 1987 and 2006 China Sampling Surveys on Disability were used to estimate the impacts of rapid ageing and the widening urban-rural gap on the prevalence of disability. Stratum specific rates of disability were estimated by 5-year age-group and type of residence. The decomposition of rates method was used to calculate the rate difference for each stratum between the two surveys. Results The crude disability rate increased from 4.89% in 1987 to 6.39% in 2006, a 1.5% increase over the 19 year period. However, after the compositional effects from the overall rates of changing age-structure in 1987 and 2006 were eliminated by standardization, the disability rate in 1987 was 6.13%, which is higher than that in 2006 (5.91%). While in 1987 the excess due to rural residence compared with urban was <1.0%, this difference increased to >1.5% by 2006, suggesting a widening disparity by type of residence. When rates were decomposed, the bulk of the disability could be attributed to ageing, and very little to rural residence. However, a wider gap in prevalence between rural and urban areas could be observed in some age groups by 2006. Conclusion The increasing number of elderly disabled persons in China and the widening discrepancy of disability prevalence between urban and rural areas may indicate that the most important priorities for disability prevention in China are to reinforce health promotion in older adults and improve health services in rural communities.
Building Accurate Associative Classifier Based on Closed Itemsets and Certainty Factor

The application of association rule mining to classification has led to a new family of classifiers which are often referred to as Associative Classifiers (ACs). An advantage of ACs is that they are rule-based and thus lend themselves to an easier interpretation. However, it is common knowledge that association rule mining typically yields a sheer number of rules defeating the purpose of a human readable model. Hence, selecting and ranking a small subset of high-quality rules without jeopardizing the classification accuracy is paramount. This article introduces a new method for building associative classifier. In this method, only association rules based on closed itemsets are used for constructing classifier. Furthermore, certainty factor is used for ranking rules in classifier. Experimental results show that the proposed associative classifier is effective.
Anticipatory Cognitive Stress Appraisal and the Acute Procoagulant Stress Response in Men

Objective: Acute mental stress elicits blood hypercoagulability. Following a transactional stress model, we investigated whether individuals who anticipate stress as more threatening, challenging, and as exceeding their coping skills show greater stress reactivity of the coagulation activation marker D-dimer, indicating fibrin generation in plasma. Methods: Forty-seven men (mean age 44 ± 14 years; mean blood pressure [MBP] 101 ± 12 mm Hg; mean body mass index [BMI] 26 ± 3 kg/m2) completed the Primary Appraisal Secondary Appraisal (PASA) scale before undergoing the Trier Social Stress Test (combination of mock job interview and mental arithmetic task). Heart rate, blood pressure, plasma catecholamines, and D-dimer levels were measured before and after stress, and during recovery up to 60 minutes poststress. Results: Hemodynamic measures, catecholamines, and D-dimer changed across all time points (p values <.001). The PASA “Stress Index” (integrated measure of transactional stress perception) correlated with total D-dimer area under the curve (AUC) between rest and 60 minutes poststress (r = 0.30, p = .050) and with D-dimer change from rest to immediately poststress (r = 0.29, p = .046). Primary appraisal (combined “threat” and “challenge”) correlated with total D-dimer AUC (r = 0.37, p = .017), D-dimer stress change (r = 0.41, p = .004), and D-dimer recovery (r = 0.32, p = .042). “Challenge” correlated more strongly with D-dimer stress change than “threat” (p = .020). Primary appraisal (&Dgr;R2 = 0.098, &bgr; = 0.37, p = .019), and particularly its subscale “challenge” (&Dgr;R2 = 0.138, &bgr; = 0.40, p = .005), predicted D-dimer stress change independently of age, BP, BMI, and catecholamine change. Conclusions: Anticipatory cognitive appraisal determined the extent of coagulation activation to and recovery from stress in men. Particularly individuals who anticipated the stressor as more challenging and also more threatening had a greater fibrin stress response. AUC = area under the curve; BMI = body mass index; CAD = coronary artery disease; EPI = epinephrine; HR = heart rate; MBP = mean blood pressure; NEPI = norepinephrine; PASA = Primary Appraisal Secondary Appraisal; TSST = Trier Social Stress Test.
Deep Neural Networks for the Recognition and Classification of Heart Murmurs Using Neuromorphic Auditory Sensors

Auscultation is one of the most used techniques for detecting cardiovascular diseases, which is one of the main causes of death in the world. Heart murmurs are the most common abnormal finding when a patient visits the physician for auscultation. These heart sounds can either be innocent, which are harmless, or abnormal, which may be a sign of a more serious heart condition. However, the accuracy rate of primary care physicians and expert cardiologists when auscultating is not good enough to avoid most of both type-I (healthy patients are sent for echocardiogram) and type-II (pathological patients are sent home without medication or treatment) errors made. In this paper, the authors present a novel convolutional neural network based tool for classifying between healthy people and pathological patients using a neuromorphic auditory sensor for FPGA that is able to decompose the audio into frequency bands in real time. For this purpose, different networks have been trained with the heart murmur information contained in heart sound recordings obtained from nine different heart sound databases sourced from multiple research groups. These samples are segmented and preprocessed using the neuromorphic auditory sensor to decompose their audio information into frequency bands and, after that, sonogram images with the same size are generated. These images have been used to train and test different convolutional neural network architectures. The best results have been obtained with a modified version of the AlexNet model, achieving 97% accuracy (specificity: 95.12%, sensitivity: 93.20%, PhysioNet/CinC Challenge 2016 score: 0.9416). This tool could aid cardiologists and primary care physicians in the auscultation process, improving the decision making task and reducing type-I and type-II errors.
A survey on measuring indirect discrimination in machine learning

Nowadays, many decisions are made using predictive models built on historical data.Predictive models may systematically discriminate groups of people even if the computing process is fair and well-intentioned. Discrimination-aware data mining studies how to make predictive models free from discrimination, when historical data, on which they are built, may be biased, incomplete, or even contain past discriminatory decisions. Discrimination refers to disadvantageous treatment of a person based on belonging to a category rather than on individual merit. In this survey we review and organize various discrimination measures that have been used for measuring discrimination in data, as well as in evaluating performance of discrimination-aware predictive models. We also discuss related measures from other disciplines, which have not been used for measuring discrimination, but potentially could be suitable for this purpose. We computationally analyze properties of selected measures. We also review and discuss measuring procedures, and present recommendations for practitioners. The primary target audience is data mining, machine learning, pattern recognition, statistical modeling researchers developing new methods for non-discriminatory predictive modeling. In addition, practitioners and policy makers would use the survey for diagnosing potential discrimination by predictive models.
Study of Physically Transient Insulating Materials as a Potential Platform for Transient Electronics and Bioelectronics

Controlled degradation and transiency of materials is of significant importance in the design and fabrication of degradable and transient biomedical and electronic devices and platforms. Here, the synthesis of programmable biodegradable and transient insulating polymer films is reported, which have sufficient physical and chemical properties to be used as substrates for the construction of transient electronics. The composite structure can be used as a means to control the dissolution and transiency rate of the polymer composite film. Experimental and computational studies demonstrate that the addition of gelatin or sucrose to a PVA polymer matrix can be used as a means to program and either slow or enhance the transiency of the composite. The dissolution of the polymer composites are fitted with inverse exponential functions of different time constants; the lower time constants are an indication of faster transiency of the polymer composite. The addition of gelatin results in larger time constants, whereas the addition of sucrose generally results in smaller time constants.
Spontaneous movement disorders in antipsychotic-naive patients with first-episode psychoses: a systematic review

Background Spontaneous movement disorders (SMDs), such as spontaneous dyskinesia and parkinsonism, have been described in patients with schizophrenia who have never been treated with antipsychotic medication. Their presence has been documented extensively in chronic schizophrenia but not at the time of illness onset. Method We performed a systematic review of studies investigating spontaneous abnormal movements elicited on clinical examination in antipsychotic-naive patients with first-episode psychosis. Results We identified a total of 13 studies. Findings suggest a spontaneous dyskinesia median rate of 9% and a spontaneous parkinsonism median rate of 17%. Information on akathisia and dystonia was limited. The presence of SMDs may be associated with negative symptoms and cognitive dysfunction. Conclusions These findings support the notion that spontaneous abnormal movements are part of a neurodysfunction intrinsic to the pathogenesis of schizophrenia. Future studies should further investigate the role of basal ganglia and extrapyramidal pathways in the pathophysiology of psychosis, with particular attention to treatment implications.