Miracle-dz/UniFAR-FTUs huggingface dataset:
Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data

Detection of SARS-CoV-2 in wastewater is an important strategy for community level surveillance. Variants of concern (VOCs) can be detected in the wastewater samples using next generation sequencing, however it can be challenging to determine the relative abundance of different VOCs since the reads cannot be assembled into complete genomes. Here, we present Alcov (abundance learning of SARS-CoV-2 variants), a tool that uses mutation frequencies in SARS-CoV-2 sequencing data to predict the distribution of VOC lineages in the sample. We used Alcov to predict the distributions of lineages from three wastewater samples which agreed well with clinical data. By predicting not just which VOCs are present, but their relative abundances in the population, Alcov extracts a more complete snapshot of the variants which are circulating in a community.
Comparison of antigen- and RT-PCR-based testing strategies for detection of SARS-CoV-2 in two high-exposure settings

Surveillance testing for infectious disease is an important tool to combat disease transmission at the population level. During the SARS-CoV-2 pandemic, RT-PCR tests have been considered the gold standard due to their high sensitivity and specificity. However, RT-PCR tests for SARS-CoV-2 have been shown to return positive results when administered to individuals who are past the infectious stage of the disease. Meanwhile, antigen-based tests are often treated as a less accurate substitute for RT-PCR, however, new evidence suggests they may better reflect infectiousness. Consequently, the two test types may each be most optimally deployed in different settings. Here, we present an epidemiological model with surveillance testing and coordinated isolation in two congregate living settings (a nursing home and a university dormitory system) that considers test metrics with respect to viral culture, a proxy for infectiousness. Simulations show that antigen-based surveillance testing coupled with isolation greatly reduces disease burden and carries a lower economic cost than RT-PCR-based strategies. Antigen and RT-PCR tests perform different functions toward the goal of reducing infectious disease burden and should be used accordingly.
The interpersonal processes of non-suicidal self-injury: A systematic review and meta-synthesis.

BACKGROUND Understanding the processes underlying non-suicidal self-injury (NSSI) is important given the negative consequences of this behaviour. Qualitative research has the potential to provide an in-depth exploration of this. There has been limited research regarding the interpersonal processes associated with NSSI; therefore, a meta-synthesis was conducted to investigate this. METHODS A search of PsycINFO, MEDLINE, Web of Science, and CINAHL electronic databases from date of inception to November 2020 was conducted. In total, 30 papers were included in the final review. A meta-ethnographic approach was utilized to synthesize the data. RESULTS Two overarching themes were found. Within 'Powerful relational dynamics', NSSI was cited as a response to participants becoming stuck in aversive or disempowering relational positions with others. Within the 'Taking matters into their own hands' subtheme, NSSI was reported as a way for participants to get interpersonal and emotional needs met. LIMITATIONS Several included papers did not comment on the researcher-participant relationship, which may have affected qualitative results. A small number of potentially eligible papers were unavailable for synthesizing. CONCLUSION Findings provide a more nuanced investigation of the interpersonal processes underlying NSSI. Consistent with relevant theories, NSSI appears to be a way of mitigating difficult interpersonal experiences or getting interpersonal needs met. NSSI may be engaged in as a substitute to other, less damaging ways to cope. An argument is made for a more empathetic understanding of NSSI and the use of relational interventions. PRACTITIONER POINTS Self-injury may occur in response to interpersonal stressors Self-injury can be a means to get interpersonal needs met Self-injury may replace other means of coping that become blocked or thwarted Emotional distress can be closely linked with interpersonal factors for this group Relational therapies may be beneficial where interpersonal processes are linked to NSSI.
P125 Sleep and fear conditioning, extinction learning and extinction recall: a systematic review and meta-analysis of polysomnographic findings

Abstract Sleep may contribute to the long-lasting consolidation and processing of emotional memories. Experimental fear conditioning and extinction paradigms model the development, maintenance, and treatment of anxiety disorders. The literature provides compelling evidence for the involvement of rapid eye movement (REM) sleep in the consolidation of such memories. This meta-analysis correlated polysomnographic sleep findings with psychophysiological reactivity to the danger (CS+) and safety stimuli (CS-), to clarify the specific role of sleep stages before and after fear conditioning, extinction learning and extinction recall. Overall, there was evidence that more pre-learning sleep stage two and less slow wave sleep was associated with higher psychophysiological reactivity to the safety stimulus during extinction learning. Preliminary evidence found here support the role of REM sleep during the post-extinction consolidation sleep phase in clinical populations with disrupted sleep, but not in healthy controls. Furthermore, the meta-regressions found that sex moderated the associations between sleep and psychophysiological reactivity throughout the paradigm providing evidence for diverging correlations in male and females. Specifically, increased post-extinction REM was associated with poorer extinction and safety recall in females while the opposite was found in males. These results have implications for future research in the role of sleep in emotional memory processing.
Data Resource Profile: The Virtual Cardio-Oncology Research Initiative (VICORI) linking national English cancer registration and cardiovascular audits

Data Resource Profile: The Virtual CardioOncology Research Initiative (VICORI) linking national English cancer registration and cardiovascular audits Michael J Sweeting ,* Clare Oliver-Williams, Lucy Teece, Catherine A Welch, Mark A de Belder, Briana Coles , Paul C Lambert, Lizz Paley, Mark J Rutherford, Lucy Elliss-Brookes, John Deanfield, Mick D Peake and David Adlam; on behalf of the VICORI Collaborative Biostatistics Research Group, Department of Health Sciences, University of Leicester, Leicester, UK, National Cancer Registration and Analysis Service, Public Health England, London, UK, National Institute for Cardiovascular Outcomes Research, Barts Health NHS Trust, London, UK, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, Institute of Cardiovascular Science, University College London, London, UK, Department of Respiratory Medicine, University of Leicester, Leicester, UK and Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
Factors influencing plasma galectin-3 concentrations in catheter-bearing hospitalized patients

Introduction: Catheters are an integral part of modern medicine although their use is not without complications. Catheter-related infection triggers a strong inflammatory reaction and has been associated with high morbidity, mortality, and healthcare costs. The clinical diagnosis of catheter-related infection is made difficult by non-specific symptoms. Investigating the alterations in biochemical parameters related to infec-tious and inflammatory processes in these patients constitute an active line of re-search. The aim of this study was to investigate factors influencing the plasma concen-tration of galectin-3 in catheter-bearing patients and to explore its potential usefulness as an index for catheter-related infections. Methods: Circulating concentrations of galectin-3, chemokine (C-C) motif ligand 2, pro-calcitonin and C-reactive protein were measured in 110 patients with a central venous catheter, 165 patients with a urinary catheter, and 72 control subjects. Results: Catheter-bearing patients had significantly higher concentrations of galectin-3 and the other markers than the control group. We identified chronic kidney disease as an independent determinant of plasma galectin-3 concentrations in patients with a central catheter, and serum creatinine concentration, cardiovascular disease and the number of days the catheter was indwelling as determinants in urinary catheter pa-tients. We also found that measuring galectin-3 in urinary catheter patients with a catheter-related infection was more accurate for diagnosis than the other parameters. At galectin-3 = 15 ng/mL, sensitivity was 90%. Conclusion: We conclude that measurement of galectin-3 concentration may be useful for assessing the inflammatory status of catheter-bearing patients and may contribute to the diagnosis of catheter-related infection in those with a urinary catheter.
Microscopic and Metagenomic Evidence for Eukaryotic Microorganisms Associated with Atacama Desert Populations of Giant Equisetum

Abstract. Understanding features that fostered the persistence of Equisetum–Earth's oldest extant vascular plant genus–since Mesozoic times and through episodes of significant global environmental change, is of current interest in view of modern challenges to plant survival. In addition to known structural and physiological adaptations, we hypothesized that microscopy and shotgun metagenomic sequencing might reveal eukaryotic microorganisms such as fungi that may aid Equisetum survival. Here, we report evidence for several lineages of eukaryotic microbes associated with giant Equisetum xylochaetum, which dominates vegetation in saline streambeds of remote valleys in the hyper-arid Atacama Desert, Chile. Plant material was collected and field-preserved at two comparatively low-disturbance sites; DNA extracted in Chile using low-shear methods was later sequenced, 18S and 28S rDNA taxonomic marker sequences were selected for SILVAngs classification, allowing comparisons to eukaryotic microorganisms previously inferred for earlier-diverging plant lineages. SEM, fluorescence microscopy, and/or LM of toluidine blue-stained sections of roots indicated protists, epiphytic and endophytic fungi, and cortical nematodes. Eukaryotic genera inferred from 18S rDNA at >100X mean sequencing depth included the ciliate Engelmanniella, hyphal chytrid Monoblepharella, predatory ascomycete Cephaliophora, a salpingoecid choanoflagellate, and an annelid worm. 23S rDNA sequences indicated ascomycete Capnodiales fungi at one site and four types of Pezizomycotina fungi at the other. No evidence for vesicular-arbuscular mycorrhizal fungi was found, but we hypothesized that Equisetum may benefit from other types of fungal associations, some possibly inherited from ancestral plant lineages.
Epidemiological approach to nematode polyparasitism occurring in a sympatric wild ruminant multi-host scenario

Abstract The epidemiology behind multi-host/multi-parasite systems is particularly interesting to investigate for a better understanding of the complex dynamics naturally occurring in wildlife populations. We aimed to approach the naturally occurring polyparasitism of gastrointestinal nematodes in a sympatric wild ruminant scenario present in south-east Spain. To this end, the gastrointestinal tract of 252 wild ruminants of four different species (red deer, Cervus elaphus; mouflon, Ovis aries musimon; Iberian ibex, Capra pyrenaica and fallow deer, Dama dama) were studied in Cazorla, Segura y Las Villas Natural Park (Andalusia, Spain). Of the analysed animals, 81.52% were positive for parasite infection and a total of 29 nematode species were identified. Out of these, 25 species were detected in at least two host species and 11 parasitized all ruminant species surveyed. The multi-host interaction between these nematodes and the four host species is discussed under the perspective of host family-based differences.
Educational interventions by nurses in caregivers with their elderly patients at home

Abstract Introduction: The home is the natural setting for the development of informal care. The work that nurses are required to develop in this context (the carer/the elderly dependent/the home) focuses on training and educational activities to assist these two groups, such as demonstrating care activities to help dependent seniors, instruction in self-care techniques and teaching strategies for the use of human and material resources. Aims: This article analyzes care education interventions performed by nurses, and the factors that facilitate, or limit, health care training. Methodological approach: This is a qualitative, descriptive study designed to be flexible and openly analytical in its approach to the research problem and the dynamic nature of the home environment. Triangulation of the methodological techniques and study subjects was applied. Results: Nursing interventions related to professional attitudes, such as encouraging communication and facilitating teaching; communication interventions in health education and counseling; and technical interventions aimed at improving access to health information and support for the informal carer. Lack of will, the advanced age of the carer, emotional state and work overload are factors that undermine care instruction, which if reversed, would become learning facilitators. The lack of time and resources in the home are the major limiting factors on care teaching, according to nurses. Evidence from our study suggests that care in the home is considered a key primary health care strategy, one in which nurses play a significant role.
Précipitation et contrainte dans le silicium implanté par hydrogène

Dans les instants qui suivent l'implantation d'ions hydrogene dans du silicium monocristallin a temperature ambiante, des defauts complexes se forment et une contrainte en compression apparait dans les plans paralleles a la surface du wafer. L'evolution thermique de ce systeme au cours du recuit conduit a la co-precipitation d'atomes d'hydrogene et de lacunes de silicium sous la forme de cavites plates (platelets) localisees dans deux familles de plans. Ces platelets sont a l'origine d'un phenomene de fracture utilise par l'industrie pour la fabrication de substrats SOI innovants et le mecanisme conduisant a leur formation doit etre approfondi. Dans ce travail, nous avons tout d'abord decrit la formation, a temperature ambiante, des complexes resultants de la rencontre entre les defauts ponctuels initialement generes par l'implantation. Le modele propose depend des concentrations et des diffusivites de ces defauts ponctuels ainsi que des energies de formation des complexes consideres. Nous avons relie ces concentrations a la contrainte generee ainsi qu'a la deformation du cristal en resultant. Des mesures experimentales de ces grandeurs nous ont permis de calibrer notre modele et de proposer une explication quant a la reaction mecanique du silicium a l'implantation d'hydrogene. Nous avons ensuite calcule la variation de l'energie libre de Gibbs du systeme consecutive a la nucleation d'un platelet. Dans un cristal non contraint, cette energie ne depend que de la famille de plans a laquelle appartient le platelet. Dans un systeme sous contrainte, nous montrons que cette energie depend egalement d'un terme decrivant le couplage entre cette contrainte et le champ de deformation genere par le platelet. Puisque ces energies controlent les taux de nucleation respectifs des differents variants d'orientation des platelets, nous avons pu calibrer notre modele a partir d'observations experimentales par TEM des occurrences des differents variants, en fonction de l'amplitude et de la direction de la contrainte, c'est-a-dire en fonction de l'orientation des wafers et de la profondeur consideree. Les modeles proposes dans ce travail, bien qu'appliques a l'implantation d'hydrogene dans le silicium, sont tout a fait generiques. Ils montrent comment contraintes et defauts interagissent en fin d'implantation et en tout debut de recuit thermique. Ils devraient permettre d'optimiser le procede industriel Smart Cut(tm) en imposant des conditions favorisant la formation de " platelets utiles " a la fracture, mais au-dela, de manipuler l'orientation de nano-precipites dans des matrices cristallines, ouvrant ainsi la voie a la fabrication controlee de nanostructures fonctionnelles.
Research Advances in Chemical Reduction of Graphene Oxide

The main types of the methods for chemical reduction and reduction mechanism of graphene oxide are briefly introduced.Furthermore,by comparing the reduction effects of several chemical reduction methods of graphene oxide,the advantages and disadvantages of chemical reduction methods including reducing capacity of reductants,reducing conditions,reduction mechanism and so on are discussed.Graphene with excellent performance can be synthesized by combining the advantages of various reductants or methods.Finally,a positive development direction in its fantastic future and other potential applications are pointed out.
An Experimental Study on the Core Autonomous System of Internet

With the continuous development of the Internet, the structure of the network has also undergone great changes. The Internet is gradually flattening, and the links between autonomous systems are increasing. Many autonomous systems realize direct transmission through Internet switching centers or related links. In order to analyze the transmission changes of the core autonomous system in the Internet. Based on the historical data of actual network routing information, this paper studies and analyzes the development of the Internet and the transmission changes of core autonomous system in the Internet. For further research and analysis, this paper designs the experimental model and related algorithms, constructs the Internet topology relationship according to the actual network routing data, and carries out independent experiments on the core autonomous system. According to the experimental results, we can find that the hierarchical structure of the Internet gradually blurred, AS the core formed dense links between local network and can provide affordable for the Internet, while the core AS the transfer function of the Internet in weakening, but the core AS the stability of the transmission of the Internet is still very important, and even play a crucial role.
A Machine Learning Approach for Suggesting Feedback in Textual Exercises in Large Courses

Open-ended textual exercises facilitate the comprehension of problem-solving skills. Students can learn from their mistakes when teachers provide individual feedback. However, courses with hundreds of students cause a heavy workload for teachers: providing individual feedback is mostly a manual, repetitive, and time-consuming activity. This paper presents CoFee, a machine learning approach designed to suggest computer-aided feedback in open-ended textual exercises. The approach uses topic modeling to split student answers into text segments and language embeddings to transform these segments. It then applies clustering to group the text segments by similarity so that the same feedback can be applied to all segments within the same cluster. We implemented this approach in a reference implementation called Athene and integrated it into Artemis. We used Athene to review 17 textual exercises in two large courses at the Technical University of Munich with 2,300 registered students and 53 teachers. On average, Athene suggested feedback for 26% of the submissions. Accordingly, 85% of these suggestions were accepted by the teachers, 5% were extended with a comment and then accepted, and 10% were changed.
Distributed Beamforming in Multi-user Multi-relay Cooperative Networks with Direct Links

We study the distributed optimal beamforming problem of a wireless amplify-and-forward (AF) multi-user and multi-relay network with minimal receive signal-to-noise ratio (SNR) limitations and per-relay transmit power budgets. In this network, direct links between sources and destinations always present. By jointly exploiting the distributed AF relay-link and direct-link signals, cooperative diversity is obtained. To achieve the above goal, we resort to minimizing the maximum relay transmit power subject to the receive SNR and per-relay transmit power constraints. Since the SNR constraints are non-convex, the problem is non-convex as well. Instead of dealing with its Lagrange dual problem just as what conventional methods usually do, we present a method which can transform the original non-convex problem into a second-order cone program (SOCP) problem. By utilizing this method, there is no need to prove the strong duality or to solve its dual problem. Thus, the optimal solution can be obtained directly. Through numerical simulations, the effects of the relay number on the min-max relay transmit power are analyzed.
Domain Experts' Interpretations of Assessment Bias in a Scaled, Online Computer Science Curriculum

Understanding inequity at scale is necessary for designing equitable online learning experiences, but also difficult. Statistical techniques like differential item functioning (DIF) can help identify whether items/questions in an assessment exhibit potential bias by disadvantaging certain groups (e.g. whether item disadvantages woman vs man of equivalent knowledge). While testing companies typically use DIF to identify items to remove, we explored how domain-experts such as curriculum designers could use DIF to better understand how to design instructional materials to better serve students from diverse groups. Using Code.org's online Computer Science Discoveries (CSD) curriculum, we analyzed 139,097 responses from 19,617 students to identify DIF by gender and race in assessment items (e.g. multiple choice questions). Of the 17 items, we identified six that disadvantaged students who reported as female when compared to students who reported as non-binary or male. We also identified that most (13) items disadvantaged AHNP (African/Black, Hispanic/Latinx, Native American/Alaskan Native, Pacific Islander) students compared to WA (white, Asian) students. We then conducted a workshop and interviews with seven curriculum designers and found that they interpreted item bias relative to an intersection of item features and student identity, the broader curriculum, and differing uses for assessments. We interpreted these findings in the broader context of using data on assessment bias to inform domain-experts' efforts to design more equitable learning experiences.
Analyzing Student Reflection Sentiments and Problem-Solving Procedures in MOOCs

Student reflection is thought to be an important part of retaining and understanding knowledge gained in a course. Using natural language processing, we analyze and interpret student reflections from Massive Open Online Courses (MOOCs) to understand the students' sentiments and problem-solving procedures. The reflections are free text responses to questions from MIT 6.00. 1x, an introductory programming MOOC. We compare different sentiment analysis methods, and conclude that the best-performing methods can robustly classify sentiment of student responses. In addition, we develop methods to analyze student problem-solving procedures using sentence parsing and topic modeling. We find our method can distinguish some common problem-solving procedures such as utilizing course resources.