Miracle-dz/UniFAR-FTUs huggingface dataset:
ControlledCycling andQuiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells

Genome editing often takes the form of either error-prone sequence disruption by non-homologous end joining (NHEJ) or sequence replacement by homology-directed repair (HDR). Although NHEJ is generally effective, HDR is often difficult in primary cells. Here, we use a combination of immunophenotyping, next-generation sequencing, and single-cell RNA sequencing to investigate and reprogram genome editing outcomes in subpopulations of adult hematopoietic stem and progenitor cells. We find that although quiescent stem-enriched cells mostly use NHEJ, non-quiescent cells with the same immunophenotype use both NHEJ and HDR. Inducing quiescence before editing results in a loss of HDR in all cell subtypes. We develop a strategy of controlled cycling and quiescence that yields a 6-fold increase in the HDR/NHEJ ratio in quiescent stem cells ex vivo and in vivo. Our results highlight the tension between editing and cellular physiology and suggest strategies to manipulate quiescent cells for research and therapeutic genome editing. DOI: https://doi.org/10.1016/j.celrep. 2020.108093 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-190901 Journal Article Published Version The following work is licensed under a Creative Commons: Attribution 4.0 International (CC BY 4.0) License. Originally published at: Shin, Jiyung J; Schröder, Markus S; Caiado, Francisco; Wyman, Stacia K; Bray, Nicolas L; Bordi, Matteo; Dewitt, Mark A; Vu, Jonathan T; Kim, Won-Tae; Hockemeyer, Dirk; Manz, Markus G; Corn, Jacob E (2020). Controlled cycling and quiescence enables efficient HDR in engraftment-enriched adult hematopoietic stem and progenitor cells. Cell Reports, 32(9):108093. DOI: https://doi.org/10.1016/j.celrep. 2020.108093
A Survey of IEEE 802.11 Protocols: Comparison and Prospective

Since the base version of IEEE 802.11 released in 1997, wireless local area network (WLAN) has been developing rapidly, and it has gone through many versions and amendments. The 802.11 protocol is now very sophisticated through 20 years of modification. Therefore, it is very hard to understand all improvements, which confuses researchers sometimes, making it not easy to discover the trend of development. This paper tries to summarize the key technologies that pushed WLAN forward among all important amendments, and then lists the latest research focus for the next generation of 802.11 family. The paper would provide assist researchers to find their field of interest.
The Closure Signature: a New Approach to Model Soft Robotic Hands

—Underactuated and compliant hands are gaining the attention of the robotic grasping community mainly due to their simple kinematics, intrinsic compliance and versatility for grasping objects in non structured environments. However, predicting, modelling, and controlling their behaviour, can present also some challenges. This abstract summarizes research efforts carried out to introduce a completely new way of representing robotic hands, that cuts ties with traditional grasp models and focuses more on the hand capabilities, rather than its kinematic structure.
Latent variable neural click models for web search

User click modeling in web search is most commonly done through probabilistic graphical models. Due to the successful use of machine learning techniques in other fields of research, it is interesting to evaluate how machine learning can be applied to click modeling. In this thesis, modeling is done using recurrent neural networks trained on a distributed representation of the state of the art user browsing model (UBM). It is further evaluated how extending this representation with a set of latent variables that are easily derivable from click logs, can affect the model’s prediction performance. Results show that a model using the original representation does not perform very well. However, the inclusion of simple variables can drastically increase the performance regarding the click prediction task. For which it manages to outperform the two chosen baseline models, which themselves are well performing already. It also leads to increased performance for the relevance prediction task, although the results are not as significant. It can be argued that the relevance prediction task is not a fair comparison to the baseline functions, due to them needing more significant amounts of data to learn the respective probabilities. However, it is favorable that the neural models manage to perform quite well using smaller amounts of data. It would be interesting to see how well such models would perform when trained on far greater data quantities than what was used in this project. Also tailoring the model for the use of LSTM, which supposedly could increase performance even more. Evaluating other representations than the one used would also be of interest, as this representation did not perform remarkably on its own.
Using routinely collected hospital data to investigate healthcare worker mobility and patient contacts within a UK hospital during the COVID-19 pandemic

Movement and contacts are central to the transmission of infectious diseases and, within the hospital setting, healthcare worker (HCW) mobility and their contact with patients play an important role in the spread of nosocomial disease. Yet data relating to HCW behaviours associated with mobility and contacts in the healthcare environment are often limited. This paper proposes a framework for integrating several electronic data sources routinely-collected by modern hospitals, to enable the measurement of HCW behaviours relevant to the transmission of infections. Using data from a London teaching hospital during the COVID-19 pandemic, we demonstrate how, at an aggregate level, electronic medical records (EMRs) and door access logs can be used to establish changes in HCW mobility and patient contacts. In addition, to show the utility of these data sources in supporting infection prevention and control (IPC), we investigate changes in the indirect connectivity of patients (resulting from shared contacts with HCWs) and spatial connectivity of floors (owing to the movements of HCWs). Average daily rates of patient contacts are computed and found to be higher throughout the pandemic compared to that pre-pandemic, while the average daily rates of HCW mobility remained stable until the second wave, where they surpassed pre-pandemic levels. The response of HCW behaviour to the pandemic was not equal between floors, whereby the highest increases in patient contacts and mobility were on floors handling the majority of COVID-19 patients. The first wave of COVID-19 patients resulted in changes to the flow of HCWs between floors, but the interconnectivity between COVID-19 and non COVID-19 wards was evident throughout the pandemic. Daily rates of indirect contact between patients provided evidence for reactive staff cohorting, whereby indirect contact rates between COVID-19 positive and negative patients were lowest during peaks in COVID-19 hospital admissions. We propose that IPC practitioners use these routinely collected data on HCW behaviour to support infection control activities and to help better protect hospital staff and patients from nosocomial outbreaks of communicable diseases.
Is Age the Most Important Risk Factor in COVID-19 Patients? The Relevance of Comorbidity Burden: A Retrospective Analysis of 10,551 Hospitalizations

Purpose To assess the contribution of age and comorbidity to the risk of critical illness in hospitalized COVID-19 patients using increasingly exhaustive tools for measuring comorbidity burden. Patients and Methods We assessed the effect of age and comorbidity burden in a retrospective, multicenter cohort of patients hospitalized due to COVID-19 in Catalonia (North-East Spain) between March 1, 2020, and January 31, 2022. Vaccinated individuals and those admitted within the first of the six COVID-19 epidemic waves were excluded from the primary analysis but were included in secondary analyses. The primary outcome was critical illness, defined as the need for invasive mechanical ventilation, transfer to the intensive care unit (ICU), or in-hospital death. Explanatory variables included age, sex, and four summary measures of comorbidity burden on admission extracted from three indices: the Charlson index (17 diagnostic group codes), the Elixhauser index and count (31 diagnostic group codes), and the Queralt DxS index (3145 diagnostic group codes). All models were adjusted by wave and center. The proportion of the effect of age attributable to comorbidity burden was assessed using a causal mediation analysis. Results The primary analysis included 10,551 hospitalizations due to COVID-19; of them, 3632 (34.4%) experienced critical illness. The frequency of critical illness increased with age and comorbidity burden on admission, irrespective of the measure used. In multivariate analyses, the effect size of age decreased with the number of diagnoses considered to estimate comorbidity burden. When adjusting for the Queralt DxS index, age showed a minimal contribution to critical illness; according to the causal mediation analysis, comorbidity burden on admission explained the 98.2% (95% CI 84.1–117.1%) of the observed effect of age on critical illness. Conclusion Comorbidity burden (when measured exhaustively) explains better than chronological age the increased risk of critical illness observed in patients hospitalized with COVID-19.
Evaluation of immunological responses to third COVID-19 vaccine among people treated with sphingosine receptor-1 modulators and anti-CD20 therapy

Background : People living with multiple sclerosis (MS) and other disorders treated with immunomodulatory therapies remain concerned about suboptimal responses to coronavirus disease 2019 (COVID-19) vaccines. Important questions persist regarding immunological response to third vaccines, particularly with respect to newer virus variants. The objective of this study is to evaluate humoral and cellular immune responses to a third COVID-19 vaccine dose in people on anti-CD20 therapy and sphingosine 1-phosphate receptor (S1PR) modulators, including Omicron-specific assays. Methods : This is an observational study evaluating immunological responses to third COVID-19 vaccine dose in participants treated with anti-CD20 agents, S1PR modulators, and healthy controls. Neutralizing antibodies against USA-WA1/2020 (WA1) and B.1. 1.529 (BA.1) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were measured before and after third vaccine. Groups were compared by one-way ANOVA with Tukey multiple comparisons. Cellular responses to spike peptide pools generated from WA1 and BA.1 were evaluated. Pre-post comparisons were made by Wilcoxon paired t-tests, inter-cohort comparisons by Mann-Whitney t-test. Results : This cohort includes 25 participants on anti-CD20 therapy, 12 on S1PR modulators, and 14 healthy controls. Among those on anti-CD20 therapy, neutralizing antibodies to WA1 were significantly reduced compared to healthy controls (ID50% GM post-vaccination of 8.1 ± 2.8 in anti-CD20 therapy group vs 452.6 ± 8.442 healthy controls, P<0.0001) and neutralizing antibodies to BA.1 were below the threshold of detection nearly universally. However, cellular responses, including to Omicron-specific peptides, were not significantly different from controls. Among those on S1PR modulators, neutralizing antibodies to WA1 were detected in a minority, and only 3/12 had neutralizing antibodies just at the limit of detection to BA.1. Cellular responses to Spike antigen in those on S1PR modulators were reduced by a factor of 100 compared to controls (median 0.0008% vs. 0.08%, p<0.001) and were not significantly “boosted” by a third injection. Conclusions : Participants on anti-CD20 and S1PR modulator therapies had impaired antibody neutralization capacity, particularly to BA.1, even after a third vaccine. T cell responses were not affected by anti-CD20 therapies, but were nearly abrogated by S1PR modulators. These results have clinical implications warranting further study.
The New Era of Virtual Reality Locomotion: A Systematic Literature Review of Techniques and a Proposed Typology

The latest technical and interaction advancements that took place in the Virtual Reality (VR) field have marked a new era, not only for VR, but also for VR locomotion. Although the latest advancements in VR locomotion have raised the interest of both researchers and users in analyzing and experiencing current VR locomotion techniques, the field of research on VR locomotion, in its new era, is still uncharted. In this work, VR locomotion is explored through a systematic literature review investigating empirical studies of VR locomotion techniques from 2014–2017. The review analyzes the VR locomotion techniques that have been studied, their interaction-related characteristics and the research topics that were addressed in these studies. Thirty-six articles were identified as relevant to the literature review, and the analysis of the articles resulted in 73 instances of 11 VR locomotion techniques, such as real-walking, walking-in-place, point and teleport, joystick-based locomotion, and more. Results showed that since the VR revival, the focus of VR locomotion research has been on VR technology and various technological aspects, overshadowing the investigation of user experience. From an interaction perspective, the majority of the utilized and studied VR locomotion techniques were found to be based on physical interaction, exploiting physical motion cues for navigation in VR environments. A significant contribution of the literature review lies in the proposed typology for VR locomotion, introducing four distinct VR locomotion types: motion-based, room scale-based, controller-based and teleportation-based locomotion.
Nuclear Reactor Thermal Expansion Reactivity Effect Determination Using Finite Element Analysis Coupled with Monte Carlo Neutron Transport Analysis

The energy released from the nuclear fission process drives thermal expansion and mechanical interactions in nuclear reactors. These phenomena cause changes in the neutron chain reaction which results in further changes in thermal expansion and mechanical interactions. Coupling finite element analysis with Monte Carlo neutron transport analysis provides a pathway to simulate the thermal expansion and mechanical interaction to determine a fundamental parameter, namely, thermal expansion temperature coefficient of reactivity. Knowing the coefficient value allows predictions of how a reactor will behave under transient conditions. Using the coupling of finite element analysis and Monte Carlo neutron transport analysis, the thermal expansion temperature coefficient of reactivity was determined for the Godiva-IV reactor (−2E−05 Δk/k/°C) and the Experimental Breeder Reactor-II (EBR-II) (−1.4E−03 $/°C). The Godiva-IV result is within 3% of the measured result. The thermal expansion and mechanical interactions within EBR-II are sufficiently complex that experimentally measuring the isolated coefficient of reactivity was not possible. However, the calculated result fits well with the integral EBR-II reactivity coefficient measurements. Coupling finite element analysis with Monte Carlo neutron transport analysis provides a powerful technique that gives reactor operators and designers greater confidence in reactor operating characteristics and safety margins.
The outcomes of limb-sparing surgery of patients with chondrosarcoma of the pelvis

1Department of Bone, Soft Tissue Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland 2Institute of Mother and Child, Warsaw, Poland 3Carolina Medical Center, Warsaw, Poland 4Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland 5Department of Diagnostic Imaging, Maria Sklodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland 6Department of Oncological Mathematics, The Maria Sklodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland
Aberystwyth University Effects of fatty acid oxidation products (‘Green odour’) on rumen bacterial populations and lipid metabolism in vitro

This study investigated the effects of green odor fatty acid oxidation products (FAOP) from cut grass on lipid metabolism and microbial ecology using in vitro incubations of rumen microorganisms. These compounds have antimicrobial roles in plant defense, and we hypothesized that they may influence rumen lipid metabolism. Further, they may partially explain the higher levels of conjugated linoleic acid cis-9, trans-11 in milk from cows grazing pasture. The first of 2 batch culture experiments screened 6 FAOP (1 hydroperoxide, 3 aldehydes, 1 ketone, and 1 alcohol) for effects on lipid profile, and in particular C18 polyunsaturated fatty acid biohydrogenation. Experiment 2 used the most potent FAOP to determine effects of varying concentrations and identify relationships with effects on microbial ecology. Batch cultures contained anaerobic buffer, rumen liquor, and FAOP to a final concentration of 100 M for experiment 1. Triplicates for each compound and controls (water addition) were incubated at 39°C for 6 h. The hydroperoxide (1,2-dimethylethyl hydroperoxide, 1,2-DMEH) and the long chain aldehyde (trans-2 decenal) had the largest effects on lipid metabolism with significant increases in C18:0 and C18:1 trans and reductions in C12:0, C14:0, C16:0, C18:1 cis, C18:2n-6, C18:3n-3, C20:0 and total branch and odd chain fatty acids compared with the control. This was associated with significantly higher biohydrogenation of C18 polyunsaturated fatty acid. In experiment 2, 1,2-DMEH was incubated at 50, 100, and 200 M for 2, 6, and 24 h. Increasing 1,2-DMEH concentration resulted in a significant linear increase in C18:1 trans-10, trans-11, conjugated linoleic acid, and C18:0 and a linear decrease in C18:2n-6 and C18:3n-3, although the scale of this response declined with time. Microbial profiling techniques showed that 1,2-DMEH at concentrations of 100 and 200 M changed the microbial community from as early as 2 h after addition, Received March 12, 2007. Accepted April 17, 2007. 1Corresponding author: michael.lee@bbsrc.ac. uk 3874 though microbial biomass remained similar. These preliminary studies have shown that FAOP can alter fatty acid biohydrogenation in the rumen. This change was associated with changes in the microbial population that were detected through DNA and branchedand odd-chain fatty acid profiling approaches.
A Contribution to the Visualization of the Diversity of Places

The availability of user-generated geographic datasets oﬀers the possibility of exploring the phenomenon “place”. In recent years researchers started some attempts to derive more information about places from the content of geo-tagged social media platforms, e. g. , Twitter and Flickr. For the communicating of the analysis results, visualization is essential, but there is less knowledge available about platial visualizations. After a short review of the literature about the extraction, approaches of analysis, and visualization of places, we will present our two methods. Based on a speciﬁc use case we will utilize density based clustering and aggregation in grid cells to demonstrate quantitative information visualization of the diversity of a place on multiple scales with pie charts.
Maximum power control of permanent magnet synchronous generator based wind power generation systems

Wind power has been one of the fastest growing and most compet itive renewable sources in the past decade. After the massive installat ion of new wind power generation systems (WPGSs), efficient and reliable operati on of them has become one main concern of the wind power industry. This thesis focu ses on improving the generation efficiency of WPGSs. The study is carried out base d on permanent magnet synchronous generator (PMSG)-WPGS, which is one main st ream WPGS due to the merits such as high reliability, high efficiency, low noi se, fast dynamic response and self-excitation on the rotor. A PMSG based wind turbine c onnects to the power grid via back to back full-rate power electronic converters and can be controlled to rotate at a varying speed in variable wind power to achieve hi gh efficiency. Chapter 1 starts an overview of typical WPGSs, including dif ferent types of wind turbines, generators and power electronic devices. Then th e three typical operation regions of a variable speed variable pitch wind turbine are p resented, i.e. the first one variable speed operation region, the second one fixed rated r o ation speed operation region, and the third one rated power operation region. In th e first operation region, the control objective is achieving maximum power extractio n from the wind, so called maximum power point tracking (MPPT). Methods for WPG Ss to achieve MPPT are reviewed. A reliable and efficient operation of a WPGS requires smooth s witching between three operation regions when the wind speed changes between th cut-in and the cut-out speed. As different region has different control st rategy, thus the switching between different operation regions is required. Non-s mooth and excessive switching between different control strategies will intro duce fatigue loads during the transitions period thus damage the mechanical part of a W PGS. Thus a smooth
Heat transfer in falling film evaporators during the industrial process of apple juice concentrate production

Falling film, shell-tube type evaporators are commonly used heat exchangers for the production of fruit juice concentrate. The main problem in the design of the exchanger is a reliable estimation of wall heat transfer coefficients for all effects in real operating conditions. Most literature sources for the overall heat transfer coefficients are based on laboratory measurements, where the tubes are usually short, no fouling exists and the flow rate is carefully adjusted. This paper shows the heat transfer estimated in real industrial operating conditions, compared to literature sources. Paper is based on the author’s own experience in designing and launching several evaporators for juice concentrate production into operation. As a summary, the design heat transfer coefficients are provided with relation to sugar content in juice concentrate.
Impact of Al content on InAs/AlSb/Al<i><sub>x</sub></i> Ga<sub>1â‹TM<i>x</i></sub> Sb tunnelling diode

Amethod to engineer the peak-to-valley ratio (PVR) by design of the epitaxial layers is presented. The impact of Al content on PVR of InAs/AlSb/AlxGa1−xSb tunnelling diode is studied. A simplified analytical model is used to explain the PVRs dependence on Al content. It was found that PVR reaches its maximum when Al content x is zero with a quantised InAs layer. The peak positions appeared in the negative differential region are effectively controlled by the applied gate bias. A PVR ratio as high as 7.1 was achieved, which is beneficial for a wide range of circuit applications. Adjusting Al content provides a new way to engineer the PVR as opposed to the conventional way of being optimised by varying barrier thicknesses or doping levels.