Miracle-dz/UniFAR-FTUs huggingface dataset:
Developments in Human Pluripotent Stem Cell Genome Engineering and in Situ Sequencing Technologies

Technology is a key driving force in the advancement of scientific discoveries. While DNA sequencing uncovered the blueprint of life encoded in the human genome, functional roles of sequence variants remain largely unknown. This thesis focuses on developing enabling technologies with broad applications for the study of genetic variations and gene regulation. Recent advances in CRISPR/Cas9-based genome engineering technology have revolutionized biomedical research. The facilitated genome editing system employs a programmable RNA that guides the Cas9 nuclease to its target DNA. Furthermore, gene targeting in human induced pluripotent stem cells (hiPSCs) offers the unprecedented potential for dissecting gene function and correcting disease mutations to fulfill the vision of personalized regenerative medicine. Despite phenomenal progress, the efficiency of targeted modifications remained low in hiPSCs. In part I of this thesis, we developed an efficient genome editing platform by reversibly integrating doxycycline-inducible Cas9 into the genome (iPS-Cas9). We characterized and optimized critical parameters for efficient targeting, generated precise mutations for disease modeling, and demonstrated the potential of multiplexed and continuous editing. Additionally, we initiated efforts to improve homology directed repair (HDR) frequency relative to nonhomologous end joining (NHEJ)
Methanol and water maser observations separate disc and outflow sources in IRAS 19410+2336

We investigate the kinematics of high mass protostellar objects within the high mass star forming region IRAS 19410+2336. We performed high angular resolution observations of 6.7-GHz methanol and 22 GHz water masers using the MERLIN (Multi-Element Radio Linked Interferometer Network) and e-MERLIN interferometers. The 6.7GHz methanol maser emission line was detected within the ∼ 16–27 km s−1 velocity range with a peak flux density ∼50 Jy. The maser spots are spread over ∼1.3 arcsec on the sky, corresponding to ∼2800 au at a distance of 2.16 kpc. These are the first astrometric measurements at 6.7 GHz in IRAS 19410+2336. The 22-GHz water maser line was imaged in 2005 and 2019 (the latter with good astrometry). Its velocities range from 13 to ∼29 km s−1. The peak flux density was found to be 18.7 Jy and 13.487 Jy in 2005, and 2019, respectively. The distribution of the water maser components is up to 165 mas, ∼350 au at 2.16 kpc. We find that the Eastern methanol masers most probably trace outflows from the region of millimetre source mm1. The water masers to the West lie in a disc (flared or interacting with outflow/infall) around another more evolved millimetre source (13-s). The maser distribution suggests that the disc lies at an angle of 60◦ or more to the plane of the sky and the observed line of sight velocities then suggest an enclosed mass between 44 M and as little as 11 M if the disc is edge-on. The Western methanol masers may be infalling.
Systemic risk and interconnectedness in Gulf Cooperation Council banking systems

Nowadays, financial interconnectedness is the main driver of systemic risk. Thus, there is a constant need for tools to assess and manage systemic risk. This paper offers an alternative model framework to measure systemic risk and examine interconnectedness between direct exposures across banking systems in the emerging markets of the Gulf Cooperation Council (GCC). To ensure consistency and efficiency of systemic risk estimates and to capture its multifaceted nature, the methodology measures systemic risk using a combination of Filtered Historical Simulation and nonparametric regression and then examines the interconnectedness using a network analysis. The results reveal that shocks originating in the banking systems in Saudi Arabia may potentially cause a cascade of failures in the banking systems of most GCC countries. The banking system in Oman, however, is robust enough to withstand any ripple effect from adverse shocks affecting GCC’s major banking systems. Such results present some policy implications for regulators and supervisors and may benefit asset managers and investors in making portfolio allocation decisions.
ASPECTOS ESPACIAIS DA EVAPOTRANSPIRAÇÃO COM O FOCO NO DIMENSIONAMENTO DE SISTEMAS DE IRRIGAÇÃO

Centro multidisciplinar, UFAC, Campus Floresta, Rua Estrada da Canela Fina, KM 12 Gleba Formoso São Francisco, CEP: 69895-000, Cruzeiro do Sul – AC, Brasil, e-email: jfvieira@hotmail.com. br Departamento de Agronomia, UFVJM, Campus JK Rodovia MGT 367, Km 583, no5000 Bairro Alto da Jacuba, CEP: 39100-000 – Diamantina – MG, Brasil, e-email: lucas.santos@ufvjm.edu. br Departamento de Agrometeorologia. Instituição: Instituto Agronômico do Paraná IAPAR. Endereço: Rodovia Celso Garcia Cid, km375, Bairro Ernani Moura Lima II, CEP: 86047-90, Londrina PR, Brasil, e-mail: danielsoares@iapar.br Departamento de Agrometeorologia. Instituição: Instituto Agronômico do Paraná IAPAR. Endereço: Rodovia Celso Garcia Cid, km375, Bairro Ernani Moura Lima II, CEP: 86047-90, Londrina PR, Brasil, e-mail: pablo@iapar.br Departamento de Engenharia de Biossistemas, USP, ESALQ, Avenida Pádua Dias, 11, Bairro Agronomia, CEP: 13418-900, Piracicaba – SP, Brasil, e-mail: mvfolega@usp.br Departamento de Engenharia de Biossistemas, USP, ESALQ, Avenida Pádua Dias, 11, Bairro: Agronomia, CEP: 13418-900, Piracicaba – SP, Brasil, e-mail: wwolf@usp.br
Reply to the interactive comment of referee#2

14 A stationary low pressure system and elevated levels of precipitable water provided a nearly continuous source 15 of precipitation over Louisiana, United States (U.S.) starting around 10 August, 2016. Precipitation was heaviest 16 in the region broadly encompassing the city of Baton Rouge, with a three3-day maximum found at a station in 17 Livingston, LA (east of Baton Rouge) from 12–14 August, 2016 (648.3 mm, 25.5 inches). The intense 18 precipitation was followed by inland flash flooding and river flooding and in subsequent days produced 19 additional backwater flooding. On 16 August, Louisiana officials reported that 30,000 people had been rescued, 20 nearly 10,600 people had slept in shelters on the night of 14 August, and at least 60,600 homes had been 21 impacted to varying degrees. As of 17 August, the floods were reported to have killed at least thirteen people. 22 As the disaster was unfolding, the Red Cross called the flooding the worst natural disaster in the U.S. since 23 Super Storm Sandy made landfall in New Jersey on 24 October, 2012. Before the floodwaters had receded, the 24 media began questioning whether this extreme event was caused by anthropogenic climate change. To provide 25 the necessary analysis to understand the potential role of anthropogenic climate change, a rapid attribution 26 analysis was launched in real-time using the best readily available observational data and high-resolution global 27 climate model simulations. 28 The objective of this study is to show the possibility of performing rapid attribution studies when both 29 observational and model data, and analysis methods are readily available upon the start. It is the authors 30 aspiration that the results be used to guide further studies of the devastating precipitation and flooding event. 31 Here we present a first estimate of how anthropogenic climate change has affected the likelihood of a 32 comparable extreme precipitation event in the Central U.S. Gulf Coast. While the flooding event of interest 33 triggering this study occurred in south Louisiana, for the purposes of our analysis, we have defined an extreme 34 precipitation event by taking the spatial maximum of annual 3-day inland maximum precipitation over the 35 region: 29–31 oN, 85–95 oW, which we refer to as the Central U.S. Gulf Coast. Using observational data, we 36 find that the observed local return time of the 12-14 August precipitation event in 2016 is about 550 years (95% 37 confidence interval (C.I.): 450-1450). The probability for an event like this to happen anywhere in the region is 38
Limitations on Protecting Information Against Quantum Adversaries

The aim of this thesis is to understand the fundamental limitations on secret key distillation in various settings of quantum key distribution. We first consider quantum steering, which is a resource for one-sided device-independent quantum key distribution. We introduce a conditional mutual information based quantifier for quantum steering, which we call intrinsic steerability. Next, we consider quantum non-locality, which is a resource for device-independent quantum key distribution. In this context, we introduce a quantifier, intrinsic non-locality, which is a monotone in the resource theory of Bell non-locality. Both these quantities are inspired by intrinsic information and squashed entanglement and are based on conditional mutual information. The idea behind these quantifiers is to suppress the correlations that can be explained by a local hidden variable or by an inaccessible quantum system, thus quantifying the remaining intrinsic correlations. We then prove various properties of these two monotones, which includes the following: monotonicity under free operations, additivity under tensor product of objects, convexity, and faithfulness, among others. Next, we prove that intrinsic steerability is an upper bound on the secret-keyagreement capacity of an assemblage, and intrinsic non-locality is an upper bound on the secret-key-agreement capacity of a quantum probability distribution. Thus we prove that these quantities are upper bounds on the achievable key rates in one-sided device-independent and device-independent quantum key distribution protocols. We also calculate these bounds for certain honest devices. The study of these upper bounds is instrumental in understanding the limitations of protocols that can be designed for various settings. These upper bounds inform us that, even if one considers the best possible protocol, there is no possibility of exceeding the upper bounds on key rates without a quantum repeater. The upper bounds introduced in this thesis are
Types and correlates of school non-attendance in students with autism spectrum disorders

School non-attendance in autism spectrum disorders has received very little attention to date. The study aimed to provide a comprehensive description of school non-attendance in students with autism spectrum disorders. Through an online survey, parents of 486 children (mean age: 11 years) reported on school attendance over 1 month and reasons for instances of non-attendance. On average, students missed 5 days of school of a possible 23 days. Persistent non-attendance (absent on 10%+ of available sessions) occurred among 43% of students. School non-attendance was associated with child older age, not living in a two-parent household, parental unemployment and, especially, attending a mainstream school. School refusal accounted for 43% of non-attendance. School exclusion and school withdrawal each accounted for 9% of absences. Truancy was almost non-existent. Non-problematic absenteeism (mostly related to medical appointments and illness) accounted for 32% of absences. Non-problematic absenteeism was more likely among those with intellectual disability, school refusal was more likely among older students and school exclusion was more likely among students from single-parent, unemployed and well-educated households. Findings suggest that school non-attendance in autism spectrum disorders is a significant issue, and that it is important to capture detail about attendance patterns and reasons for school non-attendance. Lay abstract Our study aimed to describe school non-attendance in students with autism. We conducted an online survey. Parents of 486 students (mean age: 11 years) indicated which days their child had missed school (over a period of 1 month). If the child had missed a day, the parent was asked to select a reason from a list of 15 possible reasons (this is a measure of types of school non-attendance called SNACK (School Non-Attendance ChecKlist; Heyne et al., 2019)). On average, students missed 5 days of school of a possible 23 days. Missing over 10% of school is known as persistent absence, and in our study, 43% of students experienced persistent absence. Older students, who attended mainstream schools, who did not live in a two-parent household and whose caregiver was unemployed were more likely to miss school. Looking at the reasons for absence, school refusal was the most frequent reason, accounting for 43% of absences. Nine percent of absence was due to school exclusion. Nine percent of absence was due to school withdrawal. Truancy was almost non-existent. A final reason describes non-problematic absence that is mostly due to medical appointments and illness. This type of absence accounted for 32% of absences in our study, and it was more likely in student with intellectual disability. School refusal was more likely among older students. School exclusion was more likely among students from single-parent, unemployed and well-educated households. Findings from this study help us to understand better the difficulties students with autism experience attending school.
Could artificial structures such as fish passes facilitate the establishment and spread of the ‘killer shrimp’ Dikerogammarus villosus (Crustacea: Amphipoda) in river systems?

Linkages between habitat structure, invasibility and direct species interactions were examined in a Central European river system, the Schipbeek in the Netherlands, invaded by the ‘killer shrimp’ amphipod Dikerogammarus villosus. The invader's arrival in other fresh waters is linked to declines in macroinvertebrate biodiversity, with previous studies indicating that the invader's impacts may be mediated by habitat heterogeneity and substrate type. Using an extensive 50 km field survey, potential habitat factors influencing distribution were identified. Of 12 sites surveyed, two contained fish ‘passes’ (instream sections creating faster flows via concrete structures covered in cemented rocks). It was only in these sites that D. villosus was found and then only in the fish pass areas, as opposed to the surrounding river, which, like the remaining 10 sites of the survey, was characterized by sluggish flows and a muddy/silty substrate. Gammarus roeselii was the numerically dominant amphipod in these latter areas, with no D. villosus being detected. A repeated survey more than 2 years later, revealed the same distribution pattern. Within both fish pass areas, D. villosus relative abundance was highest in faster flowing, less macrophyte dense patches, with the opposite true for G. roeselii. D. villosus numerical abundance decreased with increasing macrophyte cover in both passes. A transplant experiment indicated high survivorship of D. villosus outside fish pass areas and showed that slow-flowing watercourses with mud/silt substrates, previously deemed ‘unsuitable’, are not effective barriers to D. villosus spreading to more ‘suitable’, faster, rocky substrate watercourses. We recommend that when the location and cost-benefit analysis of instream rehabilitation structures, such as fish passes, is being considered, attention must be paid to the risk of hastening the spread of this invader. We also recommend that when monitoring programmes are designed for D. villosus in newly invaded regions, instream artificial structures should be included as part of the survey. Copyright © 2013 John Wiley & Sons, Ltd.
A Non‐Proportional Hazards Model with Hazard Ratio Functions Free from Covariate Values

A brief survey on methods to handle non‐proportional hazards in survival analysis is given with emphasis on short‐term and long‐term hazard ratio modelling. A drawback of the existing model of this nature is that except at time zero or infinity, the hazard ratio for a unit increase in the value of a covariate depends on the starting value. With two or more covariates, the hazard ratio for a unit increase in one covariate with other covariates held fixed depends in an unintended way on the values of the other covariates. We propose an alternative way to model short‐term and long‐term hazard ratios without the above drawbacks through a judicious choice of covariate‐time interactions. Under the new model, it is easier to describe the time‐varying effect of each covariate on the hazard. Nonparametric maximum likelihood estimation for the new model can be carried out in the same way as for the existing model. We also propose a product version of the existing model, which overcomes its second drawback but not the first. The advocated covariate–time interaction model provides a better fit to the Veterans Administration lung cancer data set than the original and product versions of the existing model.
Survival of advanced epithelial ovarian/fallopian tube/primary peritoneum carcinoma after high-complexity upper abdominal surgery

Most patients with epithelial ovarian cancer are diagnosed with advanced-stage disease [1]. For these patients, standard initial therapy is primary debulking surgery followed by platinum-based chemotherapy [2]. Several studies have shown that patients who have undergone optimal cytoreduction (< 1 cm residual disease) had survival advantages compared to patients who had suboptimal cytoreduction [3-6]. Bristow et al. reported in a meta-analysis that during the platinum era, primary cytoreduction improved survival outcomes [3]. Chi et al. showed that removal of all macroscopic disease is associated with improved survival. The study concluded that minimizing residual tumor is important, even if complete gross resection is not possible [4]. As surgical techniques, instruments and perioperative care develop, surgeons are able to perform maximal cytoreduction in patients with advanced stage ovarian cancer. These advances enable improvement in the rate of optimal cytoreduction and removal of metastatic sites previously thought unresectable. Optimal cytoreduction rates can vary widely among institutions and studies with a reported range of 15–85%. Achieving the highest rates of optimal cytoreduction often requires surgeons skilled in upper abdominal procedures (UAPs), such as diaphragm stripping or resection, splenectomy, distal pancreatectomy, liver resection, cholecystectomy, and resection of tumors from the porta hepatis [3, 7-9]. Aletti et al. in 2006 found an association of aggressive surgical resection, including by UAPs, with lowest residual disease and longest survival [7]. Zivanovic et al. showed that the presence of large-volume upper abdominal disease found during surgery does not preclude survival after optimal cytoreduction [10]. The present center started extensive UAPs in 2012 to improve optimal debulking rates and thereby survival rates for patients with advanced ovarian cancer. Diaphragmatic stripping and/or resection, in particular, was the most commonly performed among these upper abdominal procedures. Without these procedures, patients would have suboptimal cytoreduction for metastatic ovarian cancer in the diaphragm area. Therefore, the present authors analyzed the effects of upper abdominal procedures on progression-free survival (PFS) and overall survival (OS) in patients with FIGO Stage IIIb to IV ovarian cancer in this hospital. The authors stratified patients by initial
Physiomorphology of Soybean as Affected by Drought Stress and Nitrogen Application

Drought periods are predicted to increase in the future, putting the production of sensitive crops under serious hazards. Soybean, as a legume, is capable of partly achieving its nitrogen demands through the N2-fixation process; however, this process is inhibited by drought stress conditions. Moreover, N2-fixation might not fulfill the total N demand for soybean plants, so supplemental N-fertilizer doses might be crucial. A 3-year experiment was carried out in Debrecen, Hungary, to investigate the effects of inoculation and N-fertilizer application on the physiomorphology of soybean (cv. Boglár) under both drought stress and irrigated conditions. Results showed that, regardless of inoculation, drought negatively affected plant height, LAI, SPAD, and, to a smaller extent, NDVI. On average, increasing N-fertilizer enhanced these traits accordingly. Inoculation, on the other hand, resulted in taller plants and higher LAI values, but lower SPAD values. It could be concluded that soybean's physiomorphology is negatively influenced by drought stress and that N-fertilizer application can enhance it whether soybean plants suffer from drought stress conditions or not.
Virion Protein 24 of Ebola Virus as a Potential Drug Target

The virion protein 24 of ebola Virus is multifunctional protein. The virion protein of ebola Virus plays imperative roles in the virus life cycle. The objective of the present study was to identify the residue conservation in the virion protein 24 of various ebola viruses. The study was based on 173 sequences from Bundibugyo, Sudan, Tai Forest, Zaire and Reston ebola viruses. The virion protein 24 showed higher level of sequence conservation. On the whole, this study exposed residues which are universally conserved among different viral species. These universally conserved residues might be involved in either structure stabilizing or protein-protein interactions. The conserved residues identified in the present study in conjunction with structural analysis of virion protein 24 identified novel binding sites: Ile157, Ile161, Leu164; Leu164, Leu167; Leu150, Ile161; Ala99, Ile161; Asp205, Ser207; Phe76, His78 and Glu46, Asp48. The present study could form basis for designing universal anti-ebola drugs which are resistant to mutations arising in the future.
Words from where?

This study investigated variation in receptive L2 English vocabulary among Norwegian university students in relation to their field of study and exposure to English, both within and outside of formal education. A survey comprising the Vocabulary Levels Test (Schmitt, Schmitt, & Clapham, 2001) and questions about sources of language acquisition was completed by 189 Norwegian university students. The results indicate that vocabulary knowledge varied between students whose courses required different amounts of English reading. Extramural exposure to English was found to be a stronger predictor of vocabulary scores than formal English education. Since vocabulary knowledge is an important predictor of reading comprehension, it is important to consider how much the observed variation in vocabulary knowledge might affect academic outcomes.
Implied truth, complementary media practices, and successful atomized activism in China

While much research stereotypes mass media in authoritarian contexts as mouthpieces of the ruling party, we argue that successful social media–driven activism also requires the support of mass media, even in authoritarian contexts. To investigate the roles of social media and mass media on collective mobilization, we analyzed a case in Guangzhou, China, and conducted in-depth interviews to conceptualize the interconnected relationship between social media and mass media from the perspective of resource mobilization. Findings reveal that social media facilitated the mobilization of participants by providing less fungible and timely resources at the initial stages of collective action. However, it is the more fungible and enduring resources provided by the mass media that sustain the intensity of external pressures to the government. The complementarity between social and mass media in atomized collective action in China is in essence the configuration between exclusive and monopolized resources mediated by a middle-ground discursive mode—“implied truth. ”