Miracle-dz/UniFAR-FTUs huggingface dataset:
A workbench for the translational control of gene expression

Ribosome profiling (Ribo-seq profiling) is the most advanced tool to study the translational control of gene expression. Unfortunately, the resolution of this cutting edge technique is severely limited by a low signal to noise ratio. To tackle this issue, we introduce here a newly designed statistical method for the identification of reproducible Ribo-seq profiles. In the case of E. coli, the analysis of 2238 Ribo-seq profiles across 9 independent datasets revealed that only 11 profiles are significantly reproducible. A subsequent data quality check led us to identify one outgroup dataset. By ruling it out, the number of highly reproducible profiles could be raised to 49. Despite its surprisingly small size, this set represents a reliable workbench to both assess the quality of the data and study the factors that influence the translation process.
Risk and Cost Assessment of Nitrate Contamination in Domestic Wells

This study combines empirical predictive and economics models to estimate the cost of remediation for domestic wells exceeding suggested treatment thresholds for nitrates. A multiple logistic regression model predicted the probability of well contamination by nitrate, and a life cycle costing methodology was used to estimate costs of nitrate contamination in groundwater in two areas of Nebraska. In south-central Nebraska, 37% of wells were estimated to be at risk of exceeding a threshold of 7.5 mg/L as N, and 17% were at risk of exceeding 10 mg/L as N, the legal limit for human consumption in the United States. In an area in northeastern Nebraska, 82% of wells were at risk of exceeding the 10 mg/L as N legal threshold. Reverse osmosis Point-of-Use (POU) treatment was the option with the lowest costs for a household (3–4 individuals), with an average of $4–$164 total regional cost per household per year depending on the threshold for treatment. Ion exchange and distillation were the next most cost-effective options. At the community level (~10,000 individuals), a reverse osmosis Point-of-Entry (POE) treatment system was the most expensive option for a community due to high initial costs and ongoing operation and maintenance costs, whereas the biological denitrification system was least expensive due to economies of scale. This study demonstrates integrated modeling methods to assess water treatment costs over time associated with groundwater nitrate contamination, including quantification of at-risk wells, and identifies suitable options for treatment systems for rural households and communities based on their cost.
Government Size and Regional Capital Flows in China

Capital flows are key variables supporting the sustainability of economic growth. Based on a dataset of 31 provinces in China over 1997–2014, this paper utilizes the system generalized method of moments (System GMM) to investigate the determinants of capital flows and analyses the impact of government size on capital flows. Preliminary results show that government size exerts a negative effect on capital inflows. Specifically, government spending on capital construction and administration crowds out capital inflows significantly, while government spending on science and technology crowds in capital inflows dramatically. In addition, high quality human capital, advanced financial development, and high-level trade openness are conducive to capital inflows. High tax and labor cost impede capital inflows. These results provide proof for China’s government to reduce the size of government spending appropriately and optimize its government expenditure structure for the purpose of crowding in capital inflows.
The Effects of an Upper-Tropospheric Trough on the Heavy Rainfall Event in July 2018 over Japan

In this study, we examined the characteristics of a rainfall system that brought heavy rainfall to a broad portion of western Japan on July 5 – 8, 2018, and the role played by an upper-tropospheric trough which stayed at the rear of the extensive rainfall area during the event. The Dual-Frequency Precipitation Radar onboard the core satellite of the Global Precipitation Measurement revealed the significant contribution of rainfall with its top below 10 km, the broad spatial extent covered by stratiform rainfall, and the presence of convective rainfall embedded in the large stratiform rainfall area. These features are characteristic of well-organized rainfall systems. Based on the analysis of meteorological data, large-scale environmental conditions related to the event were found to be relatively stable and very humid throughout most of the troposphere compared with the climatology. This largescale environment, which is consistent with previous statistical results for extreme rainfall events, was present across an extensive area of Japan. We found that the trough played an important role in the maintenance of an environment favorable for rainfall organization. Dynamical ascent associated with the trough acted to produce vertical moisture flux convergence in the mid-troposphere and upper troposphere and moistened most of the troposphere in conjunction with horizontal moisture flux convergence. Humid conditions in the midto lower troposphere enhanced the development of deep convection when the lower troposphere was convectively unstable. Once deep convection was promoted in this way, convection itself could moisten the midto upper troposphere further through diabatic ascent, thereby loading the free troposphere with moisture. This synergy between the dynamical effect and the diabatic effect enhanced the conditions that allowed for a well-organized rainfall system that produced very heavy rainfall over a large portion of Japan.
A review of the impacts of pumped hydro energy storage construction on subalpine and alpine biodiversity: lessons for the Snowy Mountains pumped hydro expansion project

ABSTRACT The Australian government’s proposal to expand the Snowy Hydro Scheme to include a second pumped hydro energy storage (PHES) system, and support for feasibility studies for PHES in Tasmania, offer an opportunity to incorporate more intermittent renewable energy generation into the National Energy Market. However, the infrastructure construction required for PHES expansion may have negative effects for biodiversity in subalpine and alpine areas. To identify the potential effects of PHES on biodiversity in Kosciuszko National Park (KNP), this systematic literature review assesses: (i) the key environmental disturbances likely to arise from PHES construction; and (ii) the specific impacts of these construction processes on biodiversity in subalpine and alpine environments. We find that the effects of PHES construction-related disturbances are likely to be negative for subalpine and alpine biodiversity, with impacts including the proliferation of exotic flora, habitat loss resulting from vegetation clearing, altered landscape hydrology and reduced water quality. Management recommendations to limit these impacts are provided and further research is recommended to assess: (i) the effects of PHES on fish populations in alpine reservoirs; (ii) the utility of spoil as artificial habitat for endemic fauna; and (iii) the chemical and physical impacts of spoil dumping in alpine reservoirs.
A new mean‐field plasma edge transport model based on turbulent kinetic energy and enstrophy

The predictive capabilities of mean‐field plasma edge transport codes are significantly reduced by the empirically determined radial diffusion coefficients commonly used to account for the turbulent transport. This paper aims to assess a two‐equation model including both turbulent kinetic energy and turbulent enstrophy for an improved description of the mean‐field turbulent transport. A turbulent enstrophy equation is analytically derived for isothermal, electrostatic, two‐dimensional, interchange‐dominated ExB turbulence in the scrape‐off layer. Evaluation of this equation shows that interchange is the dominant source, while the sheath loss and viscous terms provide the main sinks of turbulent enstrophy. Transport effects turn out to be of minor importance. A model for the combined turbulent kinetic energy and enstrophy equations and the particle transport is constructed starting from a one‐equation model for the turbulent kinetic energy. The resulting two‐equation model is shown to retain the dominant dynamics of the latter while improving its scalings.
Comparison Of Three Numerical Methods For Estimating Weibull Parameters Using Weibull Distribution Model In Nigeria

There is a crucial need in Nigeria to enhance the development of wind technology in order to boost our energy supply. Adequate knowledge about the wind speed distribution becomes very essential in the establishment of Wind Energy Conversion Systems (WECS). Weibull Probability Density Function (PDF) with two parameters is widely accepted and is commonly used for modelling, characterizing and predicting wind resource and wind power, as well as assessing optimum performance of WECS. Therefore, it is paramount to precisely estimate the scale and shape parameters for all regions or sites of interest. Here, wind data from year 2000 to 2010 for four different locations (Port Harcourt, Ikeja, Kano and Jos) were analysed and the Weibull parameters was determined. The three methods employed are Mean Standard Deviation Method (MSDM), Energy Pattern Factor Method (EPFM) and Method of Moments (MOM) for estimating Weibull parameters. The method that gave the most accurate estimation of the wind speed was MSDM method, while Energy Pattern Factor Method (EPFM) is the most reliable and consistent method for estimating probability density function of wind. Keywords: Weibull Distribution, Method of Moment, Mean Standard Deviation Method, Energy Pattern Method
Long-term sick leave and work rehabilitation - prognostic factors for return to work

The main objective of this thesis is to examine individual prognostic factors for return to work (RTW) after work rehabilitation, for workers on long-term sick leave with common musculoskeletal and mental health complaints. The process of returning to work after long-term sick leave may be complex, and is often influenced by other factors than health complaints and diagnoses alone. The primary hypothesis in this thesis was that individual’s cognitions about health and illness would be central for returning to work or not, after work rehabilitation. A second hypothesis was that socioeconomic status (SES) through education or occupation would predict RTW after work rehabilitation. A third hypothesis was that the process of returning to work would be complex and differ between subgroups of work rehabilitation participants. Cognitions, such as illness perceptions and fear avoidance beliefs may be a matter of beliefs about cure, control, and expectancies, thus of coping. Coping, as defined in the Cognitive activation theory of stress (CATS), was applied in this thesis. In the CATS, coping is defined as positive response outcome expectancies, in contrast to negative response outcome expectancies (hopelessness) or no response outcome expectancies (helplessness). In Norway, comprehensive inpatient work rehabilitation may be offered to individuals on long-term sick leave. Participants in inpatient work rehabilitation programs typically have sick leave diagnoses related to musculoskeletal and mental health complaints, often characterized by non-specific conditions, mostly subjective health complaints, with few objective medical findings. Individuals with subjective health complaints may believe that their complaints are harmful and may therefore try to avoid activities they believe will harm them, such as work. Experiencing distress and poor functional ability may lead to vicious circles of hopelessness and helplessness, i.e. poor coping. Maladaptive illness perceptions and fear avoidance beliefs about work may contribute to prolonged disability and time out of work. The aim of work rehabilitation is to alter such vicious circles through positive experiences and cognitive processes, and facilitate RTW. This is done by interdisciplinary
Mucormycosis presenting as gastric perforation peritonitis in a malnourished young adult: a rare case report

A 15 year old boy presented to the surgical emergency with complaints of abdominal pain and distension for 1 day with history of bilious vomiting and not passing stools/flatus for past 2 days. He was recently diagnosed with pyogenic (bacterial) meningitis 5 weeks before for which he was undergoing treatment as a result of which he was chronically hospitalized and malnourished. He had no other co-existing illnesses or comorbidities. On examination, he was conscious, with altered mental status, poorly nourished, emaciated and had pulse rate of 115 bpm, BP-109/60 mmHg. Per abdominal examination revealed tense, distended abdomen with diffuse guarding and rigidity and absent bowel sounds. His blood reports were unremarkable and he was negative for HIV, ABSTRACT
Novel Morphological Alteration and Neural Pathway of NADPH Diaphorase Positivity in the Spinal Cord with Disc Herniation of Aged Dog: A Case Report

Neuronal lesion or injury is a traditional approach to investigate neural circuit. Is any new neural pathway or new neurodegeneration related central nerve system injury? Spinal disc herniation can cause the spinal cord injury. However, the histological examination is still lack. It happened that a case of spinal disc herniation of a 10-year old dog was examined with NADPH diaphorase (N-d) histology. We did not find the N-d neurodegenerative aberrant in the tissue of the mid-rostral lumber segment besides the metamorphoses by the compression of the disc herniation. However, the severe neuropathological changes majorly occurred in the lumbosacral spinal cord. We found more diverse neurodegenerative alterations: the aging-related N-d body (ANB), megaloneurite and N-d homogeneous formazan globule in the lumbosacral spinal cord. We also found that a new circuit pathway (intermedial collateral pathway) showed by a megaloneurite between the lateral collateral pathway and the medial collateral pathway. The enormous notch caused by spinal disc herniation located at the mid-rostral lumber segments. The aging-related neurodegeneration occurred the specific lumbosacral segments. The homogeneous formazan globule was round or oval homogeneous N-d positivity which distributed in the gray matter and dorsal column. In the medulla oblongata, ANBs were revealed in the gracile nucleus, nucleus reticularis lateralis (ventrolateral spinal trigeminal nucleus) and middle of the spinal trigeminal nucleus.
Management of safety climate and the psychosocial work environment – new challenges for occupational health and safety professionals?

It is widely accepted among practitioners and researchers that a good safety climate results in improved safety. However, there is a lack of systematic and detailed reviews summarising and evaluating the scientific evidence underpinning the accepted relationship between safety climate and injuries and accidents in a company. The current research aims to address this gap and study the association of safety climate with accidents and injury at work. Nine databases were searched for quantitative studies (in 3 languages). After eligibility and quality selection, 17 peer-reviewed papers were analysed. Quality assessment was developed applying the STROBE guidelines together with 9 appraisal criteria from Berra and colleagues (2008), Downs and Black (1998) and the appraisal tool from University of Cardiff (Weightman et al., 2004). An evaluation summary statement was then constructed analysing the strength of the evidence provided by each study. Although 15 of the 17 studies included in this review provided support (or partial support) on the association of safety climate with accidents/injuries at work, scientific evidence is still unclear on the causal relationship between these two variables. Research is needed, especially longitudinal and intervention studies, to demonstrate in detail this association which has been widely accepted in the area of Occupational Health and Safety.
Photoelectron spectroscopic studies of alkali-treated Cu(In,Ga)Se2 absorbers and simulation studies of solar cell performances

Zusammenfassung. List of abbreviations and symbols. Introduction. 1. Fundamentals of solar cells. 1.1. Basics of photovoltaics 1.1.1. Working principle of a solar cell 1.1.2. Parameters of solar cell performance 1.2. Basics of Cu(In,Ga)Se2-based thin film solar cells 1.2.1. Cu(In,Ga)Se2 crystal structure 1.2.2. Cu(In,Ga)Se2-based solar cell structure 1.2. 3. Energy band-alignment scheme of a Cu(In,Ga)Se2-based solar cell 2. Overview of state-of-the-art. 2.1. Solar cells based on Cu(In,Ga)Se2 absorbers 2.2. Solar cells based on alkali treatment of Cu(In,Ga)Se2 absorbers 3. Material characterization. 3.1. Sample preparation 3.1.1. Cu(In,Ga)Se2 absorber preparation 3.1.2. Alkali treatment of Cu(In,Ga)Se2 absorbers 3.1. 3. Buffer layer deposition 3.2. Experimental setup 3.2.1. CISSY lab setup 3.2.2. RGBL synchrotron end-station 3.2. 3. HIKE synchrotron end-station 3.3. Material characterization methods 3.3.1. Photoelectron spectroscopy (PES) analysis 3.3.2. Chemical composition analysis using XPS 3.3.3. Elemental concentration quantitative analysis using XPS 3.3. 4. Near-surface/interface and near-bulk elemental concentrations: A bi-layer model utilizing HAXPES data 3.3. 5. Valence band and work function analysis using UPS 3.3. 6. X-ray absorption spectroscopy (XAS) analysis 4. Effect of Na from soda-lime glass substrate and as post-deposition on Cu(In,Ga)Se2 absorbers. 4.1. Auger parameter analysis of Na chemical states 4.1.1. XPS core-level photoelectron and Auger peaks 4.1.2. Auger parameters and Wagner plot 4.1. 3. Separation of initial and final state contributions 4.1. 4. Na speciation iii v vii
L'évaluation des technologies de santé : les protocoles de deuxième génération

On oppose souvent la rigueur et la bonne « validité interne » des essais randomisés au pragmatisme et à la transposabilité des résultats obtenus en pratique réelle dans le cadre d’études observationnelles. A priori il est indispensable de s’entendre sur le contenu et la portée des termes utilisés. Si les essais permettent d’estimer la quantité d’effet produite par une action de santé au regard d’une autre, il est fondamental de replacer les résultats qu’ils fournissent, par rapport à l’ensemble des programmes qui pourraient être mis en place pour atteindre un objectif de santé publique déterminé. Instruments incontournables de la connaissance scientifique, ils ne peuvent à eux seul éclairer la décision politique et ne sauraient être le vecteur de l’évaluation des technologies de santé. Les bases médico-administratives et les études observationnelles apportent des informations différentes. Une enquête est dite d’observationnelle quand on peut affirmer que tout se serait passé de la même façon si l’étude n’avait pas eu lieu. Le véritable enjeu est alors de veiller à ce que ces études portent sur des populations comparables et lorsqu’elles ne le sont pas, de spécifier les techniques d’ajustement qui doivent être utilisées. Deux types d’outils semblent aujourd’hui à même de pallier les éventuelles insuffisances des schémas précédents : l’analyse de décision et les études quasi expérimentales. Cet article se propose d’étudier ces outils de deuxième génération et de les codifier pour faciliter leur mise enœuvre dans des domaines où il existe de véritables enjeux de santé publique : prévention et dépistage du cancer, maladie d’Alzheimer, troubles de l’obésité etc.
Involvement of Primary Care Providers in the Care of Hospitalized Patients

ii ACKNOWLEDGEMENTS iii CONTENTS iv 1.0 INTRODUCTION 1 2.0 BACKGROUND 3 2.1 PCPs and Hospitalists drivers of the development of hospital medicine 3 2.2 PCPs and Hospitalists in Ontario 5 2.3 The Role of PCPs and Hospitalists as their Patients are Discharged to Community 7 2.4 Managing Transitions-in-Care from Hospitalist to Community PCP 9 2.5 The Patient’s Desire for Continuity-in-Care 12 2.6 Policy Implications 13 2.7 A Proposed Conceptual Framework 15 3.0 METHODS 18 3.1 Primary Research Question: 18 3.2 Secondary Research Questions: 19 3.3 Hypothesis: 19 3.4 Databases: 20 3.4. 1 Ontario Health Insurance Plan (OHIP): 20 3.4. 2 Canada Census Area Profiles: 22 3.4. 3 Corporate Provider Database (CPDB) 22 3.4. 4 ICES Physician Database (IPDB): 22 3.4. 5 Canadian Institute of Health Information – Discharge Abstract Database (CIHI-DAD):23 3.4. 6 National Ambulatory Care Reporting System (NACRS): 24 3.4. 7 Client Agency Program Enrolment (CAPE): 24 3.4. 8 Home Care Database (HCD): 25 3.5 Variables of Interest 25 3.6 Outcome Measures 26 3.6. 1 Primary Outcome Measures, patient outcomes: 26 3.6. 2 Additional Outcome Measures, process indicators: 27 3.7 Study Design and Population 27 3.7. 1 Part One The Patients 27 3.7. 2 Part Two The Primary Care Providers (PCPs) 29 3.8 Ethics Approval 30 3.9 Power Calculation 31
Exploring strengths and weaknesses of mobility inference from mobile phone data vs. travel surveys

Origin–destination (OD) matrices serve as a basis for travel demand modelling. Traditionally, they are derived from travel surveys that collect detailed trip information but with several shortcomings. Mobile phones are regarded as a useful source of information on people’s daily mobility. This work explores the use of mobile data in the context of mobility studies by comparing matrices derived from both types of sources over the same region. The results reveal many common features in the trip information. Moreover, although the use of mobile technology may raise questions for short trips, the huge representativeness of this technology captures the mobility in OD connections extensively regardless the area. This is crucial for non-populated areas (e.g. industrial parks or educational campuses), which constitute important mobility hotspots. Based on these findings, an applicable data fusion approach to obtain the optimum accuracy from these heterogeneous sources is presented and applied.
Combined Effects of Mean Flow and Turbulence on Sediment Pickup Rate

This paper aims to explore the combined main flow and turbulence influence on sediment pickup rates by investigating four purposely devised cases, namely, (1) unobstructed flow over a plane bed; (2) unobstructed flow over a rigid‐dune bed; (3) flow obstructed by a horizontal pipe; and (4) flow obstructed by a vertical pipe. The four cases were used to represent typical scenarios of mean flow combined with turbulence of varying intensities. By analyzing the dependence of sediment pickup rate on different combinations of the mean and turbulent flow parameters, a modified densimetric Froude number, incorporating both the bulk‐averaged velocity and maximum root‐mean‐square value of the fluctuating velocity, is found to be reasonably correlated with the measured pickup rates for all the four cases. Consequently, by relating the pickup rate with the dimensionless particle diameter and the modified densimetric Froude number, a generalized equation that predicts the pickup rates under both unobstructed as well as obstructed flow conditions is obtained.