Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage

The site frequency spectrum (SFS) is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the SFS from called genotypes introduce bias when working with low-coverage sequencing data. Methods exist for addressing this issue, but suffer two problems. First, they have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multi-dimensional SFS estimation. In this article, we present a stochastic expectation-maximisation algorithm for inferring the SFS from NGS data that addresses these challenges. We show that this algorithm greatly reduces runtime and enables estimation with constant, trivial RAM usage. Further, the algorithm reduces overfitting and thereby improves downstream inference. An implementation is available at github.com/malthesr/winsfs.
Vertical and Horizontal Transmission of Cell Fusing Agent Virus in Aedes aegypti

Insect-specific flaviviruses (ISFs), are a group of nonpathogenic flaviviruses that only infect insects. ISFs can have a high prevalence in mosquito populations, but their transmission routes are not well understood. ABSTRACT Cell fusing agent virus (CFAV) is an insect-specific flavivirus (ISF) found in Aedes aegypti mosquitoes. ISFs have demonstrated the ability to modulate the infection or transmission of arboviruses such as dengue, West Nile, and Zika viruses. It is thought that vertical transmission is the main route for ISF maintenance in nature. This has been observed with CFAV, but there is evidence of horizontal and venereal transmission in other ISFs. Understanding the route of transmission can inform strategies to spread ISFs to vector populations as a method of controlling pathogenic arboviruses. We crossed individually reared male and female mosquitoes from both a naturally occurring CFAV-positive Ae. aegypti colony and its negative counterpart to provide information on maternal, paternal, and horizontal transmission. RT-PCR was used to detect CFAV in individual female pupal exuviae and was 89% sensitive, but only 42% in male pupal exuviae. This is a possible way to screen individuals for infection without destroying the adults. Female-to-male horizontal transmission was not observed during this study. However, there was a 31% transmission rate from mating pairs of CFAV-positive males to negative female mosquitoes. Maternal vertical transmission was observed with a filial infection rate of 93%. The rate of paternal transmission was 85% when the female remained negative, 61% when the female acquired CFAV horizontally, and 76% overall. Maternal and paternal transmission of CFAV could allow the introduction of this virus into wild Ae. aegypti populations through male or female mosquito releases, and thus provides a potential strategy for ISF-derived arbovirus control. IMPORTANCE Insect-specific flaviviruses (ISFs), are a group of nonpathogenic flaviviruses that only infect insects. ISFs can have a high prevalence in mosquito populations, but their transmission routes are not well understood. The results of this study confirm maternal transmission of cell fusing agent virus (CFAV) and demonstrate that paternal transmission is also highly efficient. Horizontal transmission of CFAV was also observed, aided by evaluation of the pupal infection status before mating with an infected individual. This technique of detecting infection in discarded pupae exuviae has not been evaluated previously and will be a useful tool for others in the field of studying viral transmission in mosquitoes. Identifying these routes of transmission provides information about how CFAV could be maintained in wild populations of mosquitoes and can aid future studies focusing on interactions of CFAV with their hosts and other viruses that infect mosquitoes.
Induction of Anxiety-Like Phenotypes by Knockout of Cannabinoid Type-1 Receptor in Amygdala of Marmosets

The amygdala is an important hub for the regulation of emotions, which is crucial for elucidating cellular and molecular mechanisms of many mental diseases. In the central nervous system, the endocannabinoid system plays a key role in the regulation of emotions and mainly functions through the cannabinoid type-1 receptor (CB1R), which is encoded by the Cnr1 gene. Although CB1R is highly expressed in the amygdala of non-human primates, little is known about its function. Here, we investigated the function of CB1R by knocking out the CB1R in the amygdala of adult marmosets through regional delivery of AAV-SaCas9-gRNA. We found that CB1R knockout in the amygdala of marmosets induced anxiety-like behaviors, including disrupted night sleep, agitated psychomotor activity in new environments, and reduced social desire, but had no effect on hedonic state and fear response. Moreover, CB1R-knockout marmosets exhibited up-regulated plasma cortisol levels, suggesting increased stress. These results showed that knockout of CB1R in the amygdala induced anxiety-like phenotypes in marmosets and shed new light on the mechanisms underlying the regulation of anxiety by CB1R in the amygdala of non-human primates.
Background noise: a review of the effects of background infill on urban liveability in Perth

ABSTRACT While Activity Centres and Activity Corridors are the flagships of Western Australian State Government urban infill policy, much of infill development which is being delivered is ‘background infill’ – the subdivision of suburban lots to create two to five new dwellings. This paper assesses this background infill with reference to the State Government’s goal of enhancing ‘liveability’ using criteria such as access to nature, cultural assets and public transport. The conclusion is that background infill is producing mixed results, in all of these areas, and that the policies producing such infill require attention.
The Changing Incidence of AIDS Events in Patients Receiving Highly Active Antiretroviral Therapy

after antiretroviral We describe the decline in incidence of AIDS-defining events among 12574 antiretroviral-naive individuals who started HAART in the Antiretorviral Therapy Cohort Collaboration and de-termined whether the rate of decline is similar for events with different etiologies.
Draught Caused by Large Doorways in Industrial Premises

Abstract The purpose of this study was to find out the local intensity and extent of doorway draughts, the functioning of air curtains, and the variation of the neutral pressure levels in 18 industrial premises. The doorway draught can reach the whole workspace and all the employees. At the doorline, close to the doorway, the thermal conditions can be even harsher than those outside. Air curtains significantly decrease the fluctuation of the temperature at work sites, but the functioning of the same type of air curtain varied substantially between the buildings. It seems to be impossible to estimate the height of the neutral pressure level and the air balance without measuring the pressure difference across the envelope with the ventilation both on and off. The work areas susceptible to the air flows caused by using large doors should be increasingly considered as an entity in overall planning.
Isolated Adrenocorticotrophin DeficiencyAssociated with Anti-PituitaryAntibodiesPituitaryCstShenoidalCyst and Pineal Tumor

This paper reports a rare case of isolated ACTH deficiency associated with anti-pituitary antibodies, pituitary cyst, sphenoidal cyst and pineal tumor. A 68-year-old man consulted our clinic for general fatigue. Laboratory data showed low plasma adrenocorticotrophin (ACTH) and cortisol levels with blunted responses to insulin-induced hypoglycemia and corticotrophin releasing factor (CRF). Urinary 17-OHCS was low but responded to ACTH-Z administration. No other pituitary functions were impaired. Antibodies to the cytoplasm of rat pituitary and the surface of GH3 cells were detected in the serum. The magnetic resonance imaging (MRI) showed a high signal intensity mass in the anterior pituitary and in the sphenoidal sinus in both T1 and T2 weighted images as well as a low signal intensity mass in a Ti weighted image of the pineal region. Transsphenoidal surgery was performed to resect the mass in the sphenoid sinus and in the pituitary. Pathological studies showed a benign cyst in the sphenoid sinus, and fibrous degeneration and decreased basophils in the pituitary. No infiltrative mononuclear cells were detected in the pituitary. Immunohistochemical studies revealed a decrease in the number of ACTH-producing cells in the pituitary. The patient was well maintained by glucocorticoid replacement without any growth of a possibly benign pineal tumor.
Running Head: BRIDGING THE GAP FROM PRISON TO SOCIETY 1 Bridging the Gap from Prison to Society: Evaluating the Construction of the Parole Officer’s Role and its Perceived Impact on Parolee Outcomes

For some incarcerated individuals, when they are released from prison they are released to an officer in the parole and probation department for a specified period of supervision while in the community. During this supervisory period, these individuals, also known as parolees, are able to develop pro-social skills and behaviors, which can enable them to transition into a positive and conformed member of society. For this to happen, parole officers are put in a difficult position where they are required to be both a law enforcer and a social worker. They have to monitor and manage the parolee, ensure the parolee is meeting the conditions of their supervision, and make sure that the parolee is not committing new crimes within the community. These officers also have to facilitate the parolee’s rehabilitation through cognitive and behavioral restructuring and pro-social skill building. For parolees to have the best opportunity for success while on supervision, officers must be able to balance the law enforcement and social worker aspects of the job while creating and maintaining a positive relationship with the parolee. This study examines the perceptions of parole officers from three agencies within Oregon that enable officers to utilize a balanced approach of punishment and rehabilitation in paroling. Through a social constructionist lens, this study evaluates both how officers develop, perceive, and interact with parolees and the perceived impact of the officer’s interactions on the parolee’s outcomes.
Resistance in winter wheat lines to deoxynivalenol applied into ﬂorets at ﬂowering stage and tolerance to phytotoxic effects on yield

In Europe and North America, deoxynivalenol (DON) is the most prevalent mycotoxin associated with wheat head blight caused by Fusarium graminearum and Fusarium culmorum . Because DON is toxic to plants and enhances the ability of the pathogen to spread within a spike, wheat lines with resistance to DON should be more resistant to head blight. Resistance to DON has been associated with resistance gene Fhb1 that confers resistance to spread within a spike. The objectives of this study were to determine if wheat lines resistant to head blight were also resistant to DON, if genes other than Fhb1 confer resistance to DON, and to identify lines able to ﬁll grain in the presence of DON. Susceptible controls and diverse North American and European winter wheat lines with resistance to head blight were screened for molecular markers linked to known head blight resistance genes, and evaluated in a greenhouse for resistance to DON and relative yield after application of DON to spikes at ﬂowering. Fhb1 appeared to have the unique ability to confer resistance to DON, as measured by the number of DON-bleached primary ﬂorets. However, this resistance did not protect plants from the phytotoxic effects of DON on kernel formation as measured by the relative yield of treated spikes. Furthermore, measuring the relative yield loss following DON application may be useful for identifying lines with tolerance to head blight.
What the Tweet is going on ?

We study rumors and Twitter attention focusing on acquisition transactions and how it affects market reaction, defined as abnormal trading volume, prior to announcement. We study 98 acquisition transactions, were 45 firms had tweets prior the acquisition announcement. We collected tweets one day prior to the announcement and 10 days back and perform sentiment analysis to proxy for investor sentiment. We find with statistical significance that firms with tweets has a 17.1% higher abnormal trading volume than those without, thus enable us to reject the null hypothesis. These findings are in line with previous research on how Twitter sentiment affects the stock turnover. As for how the sentiment in a tweet influences the abnormal trading volume, we can see that tweets with a neutral sentiment do affect the abnormal trading volume by 91,1% at 1% significance. We suggest by our findings that investors are not rational or rightly informed but overreact and trade on the unjustified information betting it could come true.
Validation of an audit instrument for the Unifi ed Health System

Objective: To analyze the validity and reliability of an instrument used for auditing the Unifi ed Health System (SUS). Methods: Methodological research that used the steps of adaptation of an audit instrument, recommended by the Ministry of Health, Ordinance No. 3410/2013: expert validation of content and reliability testing of the validated instrument. Results: Regarding the adequacy of the instrument, it originally had 100 items and 32 sub-items, and remained with 55 items, with their respective evaluation criteria, as well as the source of data collection, totaling 165 items of analysis. For validation of this instrument, the experts suggested changes in semantics and content in 77 (46.66%) items. The reliability test presented an agreement index of 0.85 among nurses one and two; 0.82 among nurses one and three; and 0.96 among nurses two and three, with a mean of 0.88, representing an almost perfect inter-rater agreement. Conclusion: The adequacy of the instrument, based on the current legislation and expert validation, made it concise, clear, and objective, presenting statistical consistency for use in auditing in the SUS, as demonstrated by the reliability test. por el Ministerio de Salud, Resolución nro. 3410/2013, validación del contenido por experts y prueba de confi abilidad del instrumento validado. Resultados: con relación a la adaptación del instrumento, este contenía originalmente 100 ítems y 32 subítems, y pasó a tener 55 ítems, con sus respectivos criterios de evaluación, así como la fuente de recolección de información, con un total de 165 ítems de análisis. En la validación del instrumento, los experts sugirieron cambios relacionados con la semántica y el contenido en 77 ítems (46,66%). La prueba de confi abilidad presentó un índice de concordancia de 0,85 entre las enfermeras auditoras 1 y 2; 0,82 entre las enfermeras auditoras 1 y 3, y 0,96 entre las enfermeras auditoras 2 y 3, con un promedio de 0,88, lo que representa una concordancia entre evaluadoras casi perfecta. Conclusión: la adaptación del instrumento fundamentado en la legislación vigente y la validación por experts contribuyeron para que quedara conciso, claro y objetivo, con consistencia estadística para uso en auditoría en el SUS, demostrada por la prueba de confi abilidad.
Assessment of turbulence model performance for transonic flow over an axisymmetric bump

Abstract A computational study has been performed to evaluate the predictive capabilities of some existing eddy-viscosity (both linear, LEVM, and non-linear, NLEVM) and Reynolds stress transport turbulence models (RSTM) by reference to a transonic shock-induced separated flow over a 10% axisymmetric bump. The calculations have been carried out during the course of a collaborative research programme including both UK universities and industry. The findings of the project demonstrate that improved results can be obtained for such flows by using more advanced turbulence models. For linear eddy-viscosity models, only the SST approach gave good predictions of shock location, recirculation size and pressure recovery, although this was accompanied by deficiencies in the prediction of post-shock velocity profile shape. Non-linear eddy-viscosity models, particularly at the cubic level, provided a more consistent level of agreement with experiments over the range of shock location, wall pressure and velocity profile parameters. Some improvement was also seen in the prediction of turbulence quantities, although only a move to an RSTM closure model reproduced the measured peak stress levels accurately. It was notable that the use of low-Re variants of the models (instead of wall functions) produced no significant improvement in predictions. There are, however, some shortcomings in all models, particularly in the development of flow after reattachment, which was always predicted to be too slow.
Drug-Related Problems in Type 2 Diabetes Patientswith Acute Hyperglycemia

Patients with type 2 diabetes mellitus (T2DM) and acute hyperglycemia are at risk of drug- related problem (DRPs) due to unstable haemodynamic system and multiple comorbidities that require them to take multiple medications. This retrospective study was conducted to assess the types of DRPs. The assessment of DRPs was based on Pharmaceutical Network Care Europe (PCNE) tool V5.01. Among the 239 cases of acute hyperglycemia, a total of 466 DRPs had been identified, an average of 2.66 ± 2.058 DRPs per patient. The most common DRPs encountered were potential drug-drug interactions (48.9%), drug choice problem (41.5%), dosing problem (28.2%) and adverse reaction (26.9%). Drug/dose selection (24.3%), others (13.8%) and patient/psychological factors (10.6%) were the most common causes contributing to DRPs. Therefore, early identification of risk of DRPs among T2DM patients with acute hy perglycemia may enhance the pharmacological treatment and reduce risk of mortality and morbidity.
Ultrastructure of Bacteriophages and Bacteriocins OF BACTERIOPHAGE NUCLEIC ACIDS

INTRODUCTION . 231 CLASSES OF BACTERIOLY'TIC PARTICLES . 32 ISOLATION OF BACTERIOPHAGES AND BACTERIOCINS . 232 Cuiltlirilng Methods 22. Isolatioln of a Virulelit Bacteriophage. 233 Isolatioii of a Temperate Bacteriophage. 233 Detectiont of a Bacteriociii. 233 INDUCTION OF A TEMPERATE BACTERIOPHAGE OR BACTERIOCIN . 233 PURIFICATION PROCEDURES . 234 LYsis OF A BROTH CULTURE FOR STUDYING INTRACELLULAR MULTIPLICATION . 234 ELECTRON MICROSCOPY. 2.34 Negative Stainitig . 234 Shadow-Castig . 234 Sectioniiig . 234 Rotatioiial (i/l( Liliear Ilntegraitioni Prilitilng . 234 EXAMINATION OF BACTERIOPHAGE NUCLEIC ACIDS 235 Spreading Nuicleic Acicis fr Electroii Microscopy . 235 lclelitificationt oJ Nucleic Acid Type . 235 BASIC STRUCTURE OF BACTERIOPHAGES.2. 2. 235 Architectiure of a Viruis 235 Basic Morphological Types ot Bacteriophages . 236 Syimnmetry in Bacteriophages 237 GENERAL MORPHOLOGY OF BACTERIOPHAGES. 238 Occurrence of the Basic Morphological Types iii the Bacterial Kingdom 238 Bacteriophages of Eschierichtia coli . 238 Bacteriophages of Salmontella . 242 Bacteriophages of Serratia alnd Aerobacier. 242 Bacteriophages of Pseudomonas. 242 Bacteriophages ofStalkedBacteria. 244 Staphyvlococcus alid Streptococcuis Bacteriophcges. 244 Bacterioplhages of Bacillu.s . 247 Bacteriophages of Other Geniera . 248 INFECTIV E PROCESS OF BACTERIOPHAGES . 248 MOLECULAR STRUCTURE AND INFECTIVE PROCESSES OF THE MORE IMPORTANT BACTERIO-
Inequality and welfare in quality of life among OECD countries: non-parametric treatment of ordinal data

The last few years have witnessed an increasing emphasis on going beyond GDP per capita when measuring a nation’s quality of life (QoL). Countries (e.g. UK, France, Canada, Germany, Italy, Japan, Korea, Spain) and international organizations (e.g. OECD) have been developing methods suit-able for non-income indicators. However, this involves serious measurement challenges due to: (a) multidimensionality, and (b) ordinality (i.e. unlike income these indicators do not have a natural scale). This paper is the ﬁrst summary of the methods developed in the last decade in the ﬁeld of inequality and welfare measurement to address these challenges. Next, we utilize the presented methodology and provide evidence on the ranking of OECD countries in terms of welfare and inequality in education and happiness. We ﬁnd that when dimensions are analysed separately, welfare dominance is frequent ( 42% of all comparisons in education and 31% in life satisfaction). The number drops to only 4 , 4% for bivariate dominance, which highlights the empirical relevance of multidimensional analysis. Greece, Portugal and Hungary feature the lowest joint welfare. Northern European countries are most often dominating and Southern European countries are most often dominated in both inequality and welfare analyses.
Reasons for Enrolment in the Kindergarten and Parents’ Satisfaction with Specific Elements of the Kindergarten

The importance of partnership between the parents and the kindergarten is indisputable and there are a number of works which explore the topic of the collaboration between the parents and the preschool teachers. However, there is a lack of studies that examine the parents’ perception of the satisfaction with specific elements of the kindergarten, which is an important predictor for a high-quality partnership, both in the present and in the future. In accordance with the aforementioned, the goal of this research is to determine the level of the parents’ satisfaction with specific elements of the kindergarten, as well as the reasons for the enrolment of children in the kindergarten. The research participants are the parents (N=132) of children in early childhood and preschool children who are enrolled in the kindergartens established by the local self-government in Međimurje County. The results show that the parents are predominantly satisfied with the kindergarten, and the children’s social and emotional development is highlighted as the reason for their enrolment in the educational institution.
UNSTEADY BOUNDARY LAYER TRANSITION ON A 11111111111lligium HIGH PRESSURE TURBINE ROTOR BLADE

This investigation is aimed at the experimental determination of the location, the extent, and the modes of the laminar-to-turbulent transition processes in the boundary layers of a high pressure turbine rotor blade. The results are based on time-resolved, qualitative wall shear stress data which was derived from surface hotfilm measurements. The tests were conducted in the "Windtunnel for Rotating Cascades" of the DLR in Gottingen. For the evaluation of the influence of passing wakes and shocks on the unsteady boundary layer transition, a test with undisturbed rotor inlet flow was conducted in addition to full stage tests. Two different transition modes led to a periodic-unsteady, multimoded transition on the suction side. In between two wakes, transition started in the bypass mode and terminated as separated-flow transition.