Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning Generative State Space Models for Active Inference

In this paper we investigate the active inference framework as a means to enable autonomous behavior in artificial agents. Active inference is a theoretical framework underpinning the way organisms act and observe in the real world. In active inference, agents act in order to minimize their so called free energy, or prediction error. Besides being biologically plausible, active inference has been shown to solve hard exploration problems in various simulated environments. However, these simulations typically require handcrafting a generative model for the agent. Therefore we propose to use recent advances in deep artificial neural networks to learn generative state space models from scratch, using only observation-action sequences. This way we are able to scale active inference to new and challenging problem domains, whilst still building on the theoretical backing of the free energy principle. We validate our approach on the mountain car problem to illustrate that our learnt models can indeed trade-off instrumental value and ambiguity. Furthermore, we show that generative models can also be learnt using high-dimensional pixel observations, both in the OpenAI Gym car racing environment and a real-world robotic navigation task. Finally we show that active inference based policies are an order of magnitude more sample efficient than Deep Q Networks on RL tasks.
Work Design for Performance: Expanding the Criterion Domain

INTRODUCTION The content of every job reflects a series of work design decisions made when the job is first set up or during its enactment over time. Example ‘work design’ decisions include: Which tasks should be grouped together and performed within a job? What (and how many) procedures guide the work of the job incumbent? How much control over work methods does the incumbent have? How does the job connect to tasks carried out by other individuals? Does the work have some degree of mental challenge? Sometimes these work design decisions are conscious and deliberate; other times people unconsciously or indirectly configure their work roles for themselves or others. Either way, these work design decisions create a configuration of ‘job characteristics’ for each job. Some of the most well-established job characteristics include job autonomy, job variety, job demands, and social support. Job characteristics, in turn, affect multiple outcomes, including employees’ well-being at work and outside of work, their learning and development, and potentially their performance.
The physiological effect of early pregnancy on a woman’s response to a submaximal cardiopulmonary exercise test

Given all its systemic adaptive requirements, pregnancy shares several features with physical exercise. In this pilot study, we aimed to assess the physiological response to submaximal cardiopulmonary exercise testing (CPET) in early pregnancy. In 20 healthy, pregnant women (<13 weeks gestation) and 20 healthy, non‐pregnant women, we performed a CPET with stationary cycling during a RAMP protocol until 70% of the estimated maximum heart rate (HR) of each participant. Hemodynamic and respiratory parameters were non‐invasively monitored by impedance cardiography (PhysioFlow®) and a breath‐by‐breath analyzer (OxyconTM). To compare both groups, we used linear regression analysis, adjusted for age. We observed a similar response of stroke volume, cardiac output (CO) and HR to stationary cycling in pregnant and non‐pregnant women, but a slightly lower 1‐min recovery rate of CO (−3.9 [−5.5;‐2.3] vs. −6.6 [−8.2;‐5.1] L min−1 min−1; p = .058) and HR (−38 [−47; −28] vs. −53 [−62; −44] bpm/min; p = .065) in pregnant women. We also observed a larger increase in ventilation before the ventilatory threshold (+6.2 [5.4; 7.0] vs. +3.2 [2.4; 3.9] L min−1 min−1; p < .001), lower PETCO2 values at the ventilatory threshold (33 [31; 34] vs. 36 [34; 38] mmHg; p = .042) and a larger increase of breathing frequency after the ventilatory threshold (+4.6 [2.8; 6.4] vs. +0.6 [−1.1; 2.3] breaths min−1 min−1; p = .015) in pregnant women. In conclusion, we observed a slower hemodynamic recovery and an increased ventilatory response to exercise in early pregnancy.
Systemic Mesenchymal Stem Cell-Derived Exosomes Reduce Myocardial Infarct Size: Characterization With MRI in a Porcine Model

The observations that mesenchymal stem cells (MSCs) exert cardiac protection and repair via their secretome with the active component(s) identified as exosomes underpinned our test of the efficacy of MSC exosomes in a porcine model of myocardial infarction (MI) when administered systemically by the convenient method of intravenous (IV) bolus injection. Results show that 7 days of IV exosomes results in clear reduction (30–40%) of infarct size measured at both 7 and 28 days post-MI, despite near identical release of hs Troponin T. Together with reduced infarct size, exosome treatment reduced transmurality and lessened wall thinning in the infarct zone. Exosome treated pigs showed relative preservation of LV function with significant amelioration of falls in fractional wall thickening compared with control. However, global measures of LV function were less protected by exosome treatment. It is possible that greater preservation of global LV function may have been attenuated by increased cardiac fibrosis, as T1 values showed significant increase in the exosome pigs compared to control particularly in the infarct related segments. Taken together, these results show clear effects of IV exosomes administered over 7 days to reduce infarct size with relatively preserved cardiac function compared to control treated infarct pigs.
Exact p-values for large-scale single step genome-wide association, with an application for birth weight in American Angus

BACKGROUND Single Step GBLUP (SSGBLUP) is the most comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for Genome Wide Association Studies (GWAS) without a formal framework of hypothesis testing. Our objective was to implement p-values for GWAS studies in the ssGBLUP framework, showing algorithms, computational procedures, and an application to a large beef cattle population. METHODS P-values were obtained based on the prediction error (co)variance for SNP, which uses the inverse of the coefficient matrix and formulas to compute SNP effects. RESULTS Computation of p-values took a negligible time for a dataset with almost 2 million animals in the pedigree and 1424 genotyped sires, and no inflation was observed. The SNP passing the Bonferroni threshold of 5.9 in the −log10 scale were the same as those that explained the highest proportion of additive genetic variance, but the latter was penalized (as GWAS signal) by low allele frequency. CONCLUSION The exact p-value for SSGWAS is a very general and efficient strategy for QTL detection and testing. It can be used in complex data sets such as used in animal breeding, where only a proportion of pedigreed animals are genotyped.
A Novel Homozygous Intronic Variant in TNNT2 Associates With Feline Cardiomyopathy

Background Hypertrophic cardiomyopathy (HCM) is a genetic disease of the heart and the most common cause of sudden cardiac death in the young. HCM is considered a disease of the sarcomere owing to the large number of mutations in genes encoding sarcomeric proteins. The riddle lies in discovering how these mutations lead to disease. As a result, treatments to prevent and/or treat HCM are limited to invasive surgical myectomies or ablations. The A31P variant of cardiac myosin binding protein-C, encoded by MYBPC3, was found to be more prevalent in a cohort of Maine Coon cats with HCM. However, other mutations in MYBPC3 and MYH7 have also been associated with HCM in cats of other breeds. In this study, we expand the spectrum of genes associated with HCM in cats. Results Next Generation Whole Genome sequencing was performed using DNA isolated from peripheral blood of a Maine Coon with cardiomyopathy that tested negative for the MYBPC3 A31P variant. Through risk stratification of variants, we identified a novel, homozygous intronic variant in cardiac troponin T (TNNT2). In silico analysis of the variant suggested that it may affect normal splicing of exon 3 of TNNT2. Both parents tested heterozygous for the mutation, but were unaffected by the disease. Echocardiography analyses revealed that the proband had shown early onset congestive heart failure, which is managed with a treatment regime including ACE and aldosterone inhibitors. Conclusion In summary, we are the first to demonstrate the association between TNNT2 mutations and HCM in felines, suggesting that this gene should be included in the testing panel of genes when performing genetic testing for HCM in cats.
Monitoring Steam Penetration in Channeled Instruments: An Evidence-Based Worst-Case for Practical Situations

Steam sterilization of channeled medical devices requires steam penetration into narrow channels. However, a quantitative characterization of this phenomenon in practical situations is lacking. This study evaluates the effect of load, loading pattern, and wrapping system on steam penetration into channels. We tested the hypothesis that a 70 cm tube with one closed end could be representative of the worst case for steam penetration in wrapped channeled instruments in practical conditions. A validated sterilization process was run in a sterilizer equipped with infrared sensors for the measurement of water vapor fraction (WVF). WVF values collected at the closed end of an unwrapped 70 cm reference tube were compared to those obtained at the closed end of wrapped 50 cm test tubes, representative for channeled devices in the clinical practice. The open ends of the test tubes were placed inside packs, testing the effects of different combinations of wrappings, load amounts, and pack positions. The worst case for steam penetration was experimentally defined as the condition showing the lowest WVF value during the exposure phase. WVF values at the closed end of 50 cm long tubes were affected by load amount, wrapping, and pack position. Steam penetration was higher for heavier loads in rigid containers, but lower for heavier loads in soft wrappings (pouch, non-woven fabric, and crepe). In all the tested combinations of load/wrappings related to the clinical practice the 70 cm reference tube displayed lower WVF values than the wrapped 50 cm test tubes, indicating worse steam penetration in the reference than test tubes. Our findings provide experimental evidence that a 70 cm is the worst case in all practical combinations of load and wrapping encountered in the field. The 70 cm tube is a representative for a wrapped 50 cm channel with one end closed and for a wrapped 100 cm channel with both ends open. A measuring system integrating the WVF sensor on a 70 cm tube may provide a physics-based, quantitative steam penetration test for real-time monitoring of the steam sterilization process of channeled instruments.
Item Difficulty of Fugl-Meyer Assessment for Upper Extremity in Persons With Chronic Stroke With Moderate-to-Severe Upper Limb Impairment

Background and Purpose: Limited research has been conducted with the aim of understanding which upper extremity movements are difficult for persons with severe chronic stroke. The purpose of this study was to test the structure of the Fugl-Meyer Assessment for Upper Extremity (FMA-UE) using Rasch analysis in persons with chronic stroke with moderate to severe deficits and to determine the item difficulty hierarchy. Methods: This was a secondary analysis of data from previous randomized, controlled trials, or clinical trials. The participants were 101 persons with chronic stroke with moderate to severe hemiparesis (time after onset of stroke, 1375.3 ± 1157.9 days; the 33-item FMA-UE, 31.1 ± 12.8). Principal component analysis and infit statistics were used to evaluate dimensionality. Rasch analysis using a rating scale model was performed, and item difficulty was determined. Results: Six misfit items were removed. The results showed that the 27-item FMA-UE was unidimensional. Rasch analysis showed that the movements performed within synergies were among the easiest items. Shoulder and elbow movements were among the easiest items, whereas forearm and wrist movements were among the moderately to most difficult items. Hand items spanned various difficulty levels. Discussion and Conclusions: The FMA-UE is a valid assessment tool of upper extremity motor function in persons with chronic stroke with moderate to severe deficits. The results showed that item difficulty was consistent with the stepwise recovery course proposed by Fugl-Meyer. The movements that are difficult for patients with moderate to severe chronic paresis were determined, which would enable comparison of each movement using a measure of motion difficulty in future studies.
PREVALENCE AND FACTORS ASSOCIATED WITH MUSCULOSKELETAL PAIN IN HOSPITAL CLEANING WORKERS

Objective: to assess the prevalence and the factors associated with the occurrence of musculoskeletal pain in hospital cleaning workers. Method: cross-sectional study, involving 157 outsourced workers at a university hospital in the state of Rio Grande do Sul, Brazil. The data were collected through a semistructured interview and analyzed through descriptive and analytic statistics. The prevalence of musculoskeletal pain corresponded to 70.1%, with strong and unbearable intensity in 25.5% of the cases. Results: the workers were between 19 and 34 old; 95%CI=1.03-1.27, those without time for leisure RPa=1.14; 95%CI=1.03-1.27 and those who sometimes have time for leisure RPa=1.10; 95%CI=1.02-1.20 presented higher prevalence rates for musculoskeletal pain than the other groups. Conclusion: no association was verified between musculoskeletal pain and occupational factors. Nevertheless, the workers perform their activities even with musculoskletal symptoms, which suggests attention. DESCRIPTORS: Nursing. Occupational health. Musculoskeletal pain. Hospital cleaning service. PREVALÊNCIA E FATORES ASSOCIADOS À DOR MUSCULOESQUELÉTICA EM TRABALHADORES DO SERVIÇO HOSPITALAR DE LIMPEZA
Effectiveness of African catfish pituitary extracts, dagin and water flow for optimising egg production, fertilisation and hatchability in artificial spawning of Barbus altianalis

Fish inducing hormones are widely used in commercial aquaculture to facilitate continuous supply of sufficient seed required on regular basis by the farmers. The objective of this study was to optimise production of viable eggs for improved hatchability during artificial spawning in Barbus altianalis. Two experiments were conducted, namely (i) experiment I evaluated the efficiency of using catfish pituitary extracts in spawning of second generation broodstocks compared to that of Dagin and water flow. (ii) experiment II examined ripe running females facilitated to spawn by running water only. Fish treated with pituitary extracts performed much better than those treated by Dagin with respect to fertilisation rates at 80.27 ± 39.57% (U = 66.5, p 0.05). In experiment II, hatchability and working fecundity were significantly higher when fish were striped after 4 hours (100 degree hours at 25 oC) of running water than those striped after 10 hrs (250 degree hours) but fertilization rates were not different. The findings indicate that catfish pituitary extracts are more effective in inducing B. altianalis to spawn than those treated with Dagin. However, the observations made on ripe running females in both experiments suggest that they should not be induced with any hormone. Hence, the cost of spawning could further be reduced using running water, especially in wet seasons when the majority are ripe. Key words: Eggs, hatchability, hormone, spawning
Change in Frozen Soils and its Effect on Regional Hydrology in the Upper Heihe Basin, the Northeast Qinghai-Tibetan Plateau

Abstract. Frozen ground has an important role in regional hydrological cycle and ecosystem, especially on the Qinghai-Tibetan Plateau, which is characterized by high elevation and a dry climate. This study modified a distributed physically-based hydrological model and applied it to simulate the long-term (from 1961 to 2013) change of frozen ground and its effect on hydrology in the upper Heihe basin located at Northeast Qinghai-Tibetan Plateau. The model was validated carefully against data obtained from multiple ground-based observations. The model results showed that the permafrost area shrank by 9.5 % (approximately 600 km2), especially in areas with elevation between 3500 m and 3900 m. The maximum frozen depth of seasonally frozen ground decreased at a rate of approximately 4.1 cm/10 yr, and the active layer depth over the permafrost increased by about 2.2 cm/10 yr. Runoff increased significantly during cold seasons (November–March) due to the increase in liquid soil moisture caused by rising soil temperature. Areas where permafrost changed into the seasonally frozen ground at high elevation showed especially large changes in runoff. Annual runoff increased due to increased precipitation, the base flow increased due to permafrost degradation, and the actual evapotranspiration increased significantly due to increased precipitation and soil warming. The groundwater storage showed an increasing trend, which indicated that the groundwater recharge was enhanced due to the degradation of permafrost in the study area.
The COPD (Chronic Obstructive Pulmonary Disease) Assessment Test: Assessment of Therapeutic Outcomes of Patients at Private Hospitals in Yogyakarta

Introduction: Chronic obstruction pulmonary disease (COPD) is a chronic airflow disorder along with decreasing health status. COPD assessment test (CAT) is commonly used to assess the health status of patients and their medical results. The aim of this study was to assess the therapeutic outcomes in patients with COPD using CAT in private hospitals in Yogyakarta. Materials and Methods: This was a cross-sectional study involving 156 patients, aged >40 years who had completed the CAT questionnaire. CAT scores were categorized into four groups and consisted of eight items: cough, phlegm, chest tightness, breathlessness going up hills/stairs, activity limitations at home, confidence leaving home, sleep, and energy. The four categories were successful therapy (CAT scores <10), moderately successful CAT 10–19), less successful (CAT scores 20–30), and unsuccessful (CAT score >30). The study was conducted from April to August 2018 at two Private Hospitals in Yogyakarta followed by descriptive-analytical data processing and chi-square analysis. Results: The therapeutic outcomes of COPD were 30.13% successful (CAT score: <10), 60.26% moderately successful (CAT score: 10–19), 9.62% less successful (CAT score: 20–30), and there were no patients with unsuccessful therapy. The majority of patients had moderate airflow severity. Exacerbation condition, severity level, and type of therapy showed a significant result (P < 0.05) toward therapy results with COPD measurement, and from eight CAT items, it was identified that 37.8% of respondents had breathlessness going up hills/stairs. Conclusion: CAT can assess the therapeutic outcomes and COPD patient’s health status with moderately successful therapy (CAT score 10–19) in more than sixty percent of respondents.
Molecular Detection of Ugandan Passiflora Virus Infecting Passionfruit (Passiflora edulis sims) in Rwanda

The study aimed at identifying the pathogen associated with passionfruit woodiness disease in Rwanda. Field work was conducted in Rwanda while, laboratory aspects were carried out in Biosciences for eastern and central Africa-International Livestock Research Institute Hub, Nairobi, Kenya. Duration of the study was from September 2012 to May 2013. Two hundred and one leaf samples exhibiting virus-like symptoms were collected from farmer’s fields in Nyamagabe, Ngororero and Gicumbi district found in South, West and North provinces of Rwanda, respectively. Virus detection was done using enzyme-linked immunosorbent assay and reverse-transcription polymerase chain reaction. Virus-like symptoms observed in the field included; leaf mosaic, crinkle, distortion, fruit woodiness and malformations. Ugandan passiflora virus was detected in 70% of the positive samples and other unidentified potyviruses. The incidence of virus infection was highest in North at 45.8% and lowest in West province at 18.7%. Partial amino acid sequences of the coat protein of 169 residues were used to determine the identity of the associated virus. Sequences obtained were highly similar and displayed features typical of potyviruses with 93-100% identity. Comparisons of these sequences with those of other existing potyviruses indicated highest identity (94-100%) to Ugandan passiflora virus isolates from Uganda. Sequences of four Rwandan isolates are deposited in Genbank: isolate RW10 (Accession No. MK132862), RW23 (MK132863), RW104 (MK132864) and RW140 (MK132865). This study confirms presence of the Ugandan passiflora virus in the country. This necessitates the need for production and use of virus-free planting materials, development of virus resistant genotypes and adoption of efficient seed certification systems.
Characterization of Minor Millets (Panicum sumatrense and Eleusine coracana) for Trait Related to Moisture Stress Tolerance

Drought stress is one of the abiotic stresses which may alter plant growth, metabolism and yield. Water stress limits the growth, productivity and quality of agricultural crops in the world. Water Stress is not only due to the scarcity of water but also due other factors such as salinity, high temperatures and severe cold that make plants not able to absorb enough water from soil to grow well and this is called physiological drought that leads to a series of disorders in physiological and biochemical processes. Millets are resilient to extreme environmental conditions especially to inadequate moisture and are rich in nutrients. The aim of this research was to analyze the effects of water stress on relative water content, proline, soluble carbohydrates and chlorophyll content of minor millet genotypes under control conditions. The photosynthetic pigments like chlorophyll a, chlorophyll b and total chlorophyll decreased and the biochemical components like, proline, leaf protein and carbohydrate increased under water stress. In this study little millet genotypes showed minimum decrease in chlorophyll content and maximum increase in proline, protein and carbohydrate content when compared to the previously reported tolerant millet genotype. This study suggested the little millet ( Panicum sumatrense ) genotype RLM 37 having drought tolerant adaptive mechanism and better performance under water stress. water Abstract
PconsC4: fast, free, easy, and accurate contact predictions

Motivation Residue contact prediction was revolutionized recently by the introduction of direct coupling analysis (DCA). Further improvements, in particular for small families, have been obtained by the combination of DCA and deep learning methods. However, existing deep learning contact prediction methods often rely on a number of external programs and are therefore computationally expensive. Results Here, we introduce a novel contact predictor, PconsC4, which performs on par with state of the art methods. PconsC4 is heavily optimized, does not use any external programs and therefore is significantly faster and easier to use than other methods. Availability PconsC4 is freely available under the GPL license from https://github.com/ElofssonLab/PconsC4. Installation is easy using the pip command and works on any system with Python 3.5 or later and a modern GCC compiler. Contact arne@bioinfo.se
Electron diffraction techniques

S. Amelinckx & D. van Dyck: EM imaging and diffraction contrast K. Yagi: Rheed and REM J. Gjonnes: Disorder and defect scattering S. Amelinckx & D. van Dyck: Electron diffraction effects due to modulated structures M. Carr & C. Lyman: Identifications of unknowns Index.