Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Knowledge Graphs to Plausibly Infer Missing Associations in EMR Data

Electronic Medical Records (EMRs) are increasingly being deployed at primary points of care and clinics for digital record keeping, increasing productivity and improving communication. In practice, however, there still exists an often incomplete picture of patient profiles, not only because of disconnected EMR systems but also due to incomplete EMR data entry - often caused by clinician time constraints and lack of data entry restrictions. To complete a patient's partial EMR data, we plausibly infer missing causal associations between medical EMR concepts, such as diagnoses and treatments, for situations that lack sufficient raw data to enable machine learning methods. We follow a knowledge-based approach, where we leverage open medical knowledge sources such as SNOMED-CT and ICD, combined with knowledge-based reasoning with explainable inferences, to infer clinical encounter information from incomplete medical records. To bootstrap this process, we apply a semantic Extract-Transform-Load process to convert an EMR database into an enriched domain-specific Knowledge Graph.
A Multi-User Terminology Mapping Toolbox

Semantic interoperability is a major challenge in multi-center data sharing projects, a challenge that the German Initiative for Medical Informatics is taking up. With respect to laboratory data, enriching site-specific tests and measurements with LOINC codes appears to be a crucial step in supporting cross-institutional research. However, this effort is very time-consuming, as it requires expert knowledge of local site specifics. To ease this process, we developed a generic manual collaborative terminology mapping tool, the MIRACUM Mapper. It allows the creation of arbitrary mapping workflows involving different user roles. A mapping workflow with two user roles has been implemented at University Hospital Erlangen to support the local LOINC mapping. Additionally, the MIRACUM LabVisualizeR provides summary statistics and visualizations of analyte data. We developed a toolbox that facilitates the collaborative creation of mappings and streamlines the review as well as the validation process. The two tools are available under an open source license.
Views from Multidisciplinary Oncology Clinicians on Strengthening Cancer Care Delivery Systems in Tanzania

Abstract Background In response to the increasing burden of cancer in Tanzania, the Ministry of Health, Community Development, Gender, Elderly and Children launched National Cancer Treatment Guidelines (TNCTG) in February 2020. The guidelines aimed to improve and standardize oncology care in the country. At Ocean Road Cancer Institute (ORCI), we developed a theory‐informed implementation strategy to promote guideline‐concordant care. As part of the situation analysis for implementation strategy development, we conducted focus group discussions to evaluate clinical systems and contextual factors that influence guideline‐based practice prior to the launch of the TNCTG. Materials and Methods In June 2019, three focus group discussions were conducted with a total of 21 oncology clinicians at ORCI, stratified by profession. A discussion guide was used to stimulate dialogue about facilitators and barriers to delivery of guideline‐concordant care. Discussions were audio recorded, transcribed, translated, and analyzed using thematic framework analysis. Results Participants identified factors both within the inner context of ORCI clinical systems and outside of ORCI. Themes within the clinical systems included capacity and infrastructure, information technology, communication, efficiency, and quality of services provided. Contextual factors external to ORCI included interinstitutional coordination, oncology capacity in peripheral hospitals, public awareness and beliefs, and financial barriers. Participants provided pragmatic suggestions for strengthening cancer care delivery in Tanzania. Conclusion Our results highlight several barriers and facilitators within and outside of the clinical systems at ORCI that may affect uptake of the TNCTG. Our findings were used to inform a broader guideline implementation strategy, in an effort to improve uptake of the TNCTGs at ORCI. Implications for Practice This study provides an assessment of cancer care delivery systems in a low resource setting from the unique perspectives of local multidisciplinary oncology clinicians. Situational analysis of contextual factors that are likely to influence guideline implementation outcomes is the first step of developing an implementation strategy for cancer treatment guidelines. Many of the barriers identified in this study represent actionable targets that will inform the next phases of our implementation strategy for guideline‐concordant cancer care in Tanzania and comparable settings.
Improved plant cytosine base editors with high editing activity, purity, and specificity

Summary Cytosine base editors (CBEs) are great additions to the expanding genome editing toolbox. To improve C‐to‐T base editing in plants, we first compared seven cytidine deaminases in the BE3‐like configuration in rice. We found A3A/Y130F‐CBE_V01 resulted in the highest C‐to‐T base editing efficiency in both rice and Arabidopsis. Furthermore, we demonstrated this A3A/Y130F cytidine deaminase could be used to improve iSpyMacCas9‐mediated C‐to‐T base editing at A‐rich PAMs. To showcase its applications, we first applied A3A/Y130F‐CBE_V01 for multiplexed editing to generate microRNA‐resistant mRNA transcripts as well as pre‐mature stop codons in multiple seed trait genes. In addition, we harnessed A3A/Y130F‐CBE_V01 for efficient artificial evolution of novel ALS and EPSPS alleles which conferred herbicide resistance in rice. To further improve C‐to‐T base editing, multiple CBE_V02, CBE_V03 and CBE_V04 systems were developed and tested in rice protoplasts. The CBE_V04 systems were found to have improved editing activity and purity with focal recruitment of more uracil DNA glycosylase inhibitors (UGIs) by the engineered single guide RNA 2.0 scaffold. Finally, we used whole‐genome sequencing (WGS) to compare six CBE_V01 systems and four CBE_V04 systems for genome‐wide off‐target effects in rice. Different levels of cytidine deaminase‐dependent and sgRNA‐independent off‐target effects were indeed revealed by WGS among edited lines by these CBE systems. We also investigated genome‐wide sgRNA‐dependent off‐target effects by different CBEs in rice. This comprehensive study compared 21 different CBE systems, and benchmarked PmCDA1‐CBE_V04 and A3A/Y130F‐CBE_V04 as next‐generation plant CBEs with high editing efficiency, purity, and specificity.
Savings in sensorimotor learning during balance-challenged walking but not reaching.

Safe and successful motor performance relies on the ability to adapt to physiological and environmental change and retain what is learned. An open question is what factors maximize this retention? One overlooked factor is the degree to which balance is challenged during learning. We propose that the greater need for control and/or perceived threat of falling or injury associated with balance-challenging tasks increases the value assigned to maintaining a learned visuomotor mapping (i.e., the new relationship between visual input and motor output). And we propose that a greater-valued mapping is a more retainable mapping, as it serves to benefit future motor performance. Thus, we tested the hypothesis that challenging balance enhances motor memory, reflected by greater recall and faster relearning (i.e., savings). Four groups of participants adapted to a novel visuomotor mapping induced by prism lenses while performing a reaching or walking task, with and without an additional balance challenge. We found that challenging balance did not disrupt visuomotor adaptation during reaching or walking. We then probed recall and savings by having participants repeat the adaptation protocol one week later. For reaching, we found evidence of initial recall, though neither group demonstrated savings upon re-exposure to the prisms. In contrast, both walking groups demonstrated significant initial recall and savings. Additionally, we found that challenging balance significantly enhanced savings during walking. Taken together, our results demonstrate the robustness of motor memories formed during walking and highlight the potential influence of balance control on sensorimotor learning.
Preoptic BRS3 neurons increase body temperature and heart rate via multiple pathways

The preoptic area (POA) is a key region controlling body temperature (Tb), dictating thermogenic, cardiovascular, and behavioral responses to regulate Tb. Known POA neuronal populations reduce Tb when activated; a population that increases Tb upon activation has not yet been reported. We now identify bombesin-like receptor 3 (BRS3)-expressing POA (POABRS3) neurons as having this missing functionality. BRS3 is an orphan receptor that regulates energy and cardiovascular homeostasis, but the relevant neural circuits are incompletely understood. In mice, we demonstrate that POABRS3 neuronal activation increases Tb, heart rate, and blood pressure sympathetically, via projections to the paraventricular nucleus of the hypothalamus and dorsomedial hypothalamus. Acute POABRS3 inhibition reduces Tb. Long-term inactivation of POABRS3 neurons increased Tb variability with exaggerated Tb changes, overshooting both increases and decreases in Tb set point. BRS3 marks preoptic populations that regulate Tb and heart rate, contribute to cold-defense and fine-tune feedback control of Tb. These findings advance understanding of homeothermy, a defining feature of mammalian biology. Graphical abstract
Adjuvant Temozolomide for the Treatment of Glioblastoma: A Meta-analysis of Randomized Controlled Studies

Introduction The efficacy of adjuvant temozolomide to radiotherapy for glioblastoma remained elusive. This meta-analysis aimed to explore the influence of radiotherapy plus adjuvant temozolomide on the efficacy and safety for glioblastoma. Methods We have searched several databases including PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases through November 2020 and included randomized controlled trials assessing the efficacy and safety of adjuvant temozolomide to radiotherapy for glioblastoma. Results Seven randomized controlled trials and 1900 patients were included in the meta-analysis. Overall, compared with radiotherapy for glioblastoma, adjuvant temozolomide was associated with significantly increased survival rate [odds ratio (OR), 4.04; 95% confidence interval (CI), 2.61–6.24; P < 0.00001], median progression-free survival (mean difference, 0.55; 95% CI, 0.03–1.07; P = 0.04), and hematological complications (OR, 4.12; 95% CI, 1.43–11.88; P = 0.009), but revealed no remarkable influence on adverse events (OR, 0.87; 95% CI, 0.36–2.09; P = 0.75) or serious adverse events (OR, 2.20; 95% CI, 0.55–8.70; P = 0.26). Conclusions Adjuvant temozolomide in combination with radiotherapy may improve the treatment efficacy for glioblastoma.
In-vitro anti-denaturation and antibacterial activities of Zizyphus oenoplia

Zizyphus oenoplia mill belongs to the family Rhamnaceae. The fruits of the plant are used as stomach-ache pills and root bark decoction is used to promote the healing of fresh wounds. Plant has shown the presence of cyclopeptide alkaloids. Aerial parts of the plant were reported to have anti-inflammatory and anticholinergic activities. Bark and leaves of the plant were reported for antibacterial activity. No biological and antibacterial activities were reported on root part of Zizyphus oenoplia. The aim of the study was to investigate the Anti-denaturation and antibacteriial activities for various extracts of the Zizyphus oenoplia. Root part of Zizyphus oenoplia was extracted with ethyl acetate, 90% ethanol and water using soxhlet apparatus. The solvents were evaporated under reduced pressure below 400C using rotary evaporator to obtain dry extracts. These crude extracts were subjected to investigation for anti-denaturation study and antibacterial study by using a method designed by William’s et al and agar ditch diffusion method respectively. Phytochemical analysis revealed the presence of carbohydrates, alkaloids, phenolic compounds, tannins and saponins. All the extracts of Zizyphus oenoplia protected Bovine Serum Albumin (BSA) from denaturation more than 97% at 1μg/ml concentration. Only ethanolic extract showed antibacterial activity against Staphylococus aureus
Teacher Facilitation of Elementary Science Discourse after a Professional Development Initiative

This article reports on changes in science discourse practices of four teachers who participated in an extended professional development (PD) program. Teachers were selected for their different patterns of improvement in the quality of their classroom discourse during their participation in the program. Analyses of their practices to support student discourse focused on “talk structures” and “teacher talk moves,” identified through fine-grained coding of these lesson features in classroom videos. All teachers increased their use of interactive talk structures and the cognitive demand of the talk moves they used while facilitating discussion. At the same time, there was considerable diversity in their improvements. Analyses of interviews and surveys indicate that they adopted pedagogical tools introduced in the PD program. We discuss the relationship between changes in their practice and features of the PD and suggest implications for PD and research.
A Network Traffic Processing Library for ICS Anomaly Detection

Anomaly detection in industrial control systems based on traffic monitoring is one of the key components in securing these critical cyber-physical environments. Many anomaly detection methods have been proposed in the past decade. They are based on various principles stemming from signature detection, statistical analysis, or machine learning. Because of the lack of ICS communication datasets, their evaluation and mainly comparing their performance is problematic. If provided as a prototype implementation, the methods are implemented in various languages and require different input formats. In the present paper, we propose a library that can process ICS communication, extract required information, e.g., various packet-level or flow-level features, and provide the data to a user-specified anomaly detection method. It is possible to integrate the library in the system that automates the entire processing pipeline enabling us to conduct experiments with different methods while saving the time needed for manual data preparation.
Building Air Quality Monitoring IoT Platform

This article proposes architecture of the IoT solution to measure air quality in urban areas. Paper includes design of simple ESP-based measuring devices which send raw data to local nodes over CoAP protocol. These nodes could be connected to a centralized root for further processing, archiving and distributing. The chosen criteria are low power consumption, low data exchange to keep devices cheap to build and maintain. The solution is mainly aimed to be used in amateur or community driven projects.
Supporting Autonomous Vehicle Applications on the Heterogeneous System Architecture

The contemporary processors are unable to meet the increasing data-intensive and computation-demanding requirements in autonomous vehicle software applications. Recently, the new Heterogeneous System Architecture (HSA) has emerged as a promising solution to meet these requirements. The HSA reduces the latency of data exchange between the compute units and cache-coherent shared memory, which is not supported by the non-HSA compliant heterogeneous platforms with acceleration support. The main goal of the paper is to investigate the performance gain by the HSA and conduct a comparative evaluation of the HSA and non-HSA compliant heterogeneous platforms. The paper aims at evaluating these platforms by using two computation-intensive software functions in autonomous vehicles, namely the object detection and vehicle movement. In order to achieve this goal, the CUDA-accelerated source code of the functions is ported from a non-HSA compliant heterogeneous platform to the HSA platform. In this regard, the paper presents the architecture of a proof-of-concept prototype and provides evaluation using the prototype.
On Sustainability for Offset Based Response-Time Analysis

It is known that offsets in general are not sustainable, i.e., if offsets in a system are modified it is not trivial to determine if this affects schedulability or not. In this paper we investigate if there are situations where offsets can be deemed sustainable, i.e., situations where one can safely modify an offset without impairing schedulability. We introduce, for the approximate Response-Time Analysis, a concept of a subsumes relation between demand bound functions and show that if offsets are modified in such a way that the modified demand bound function is subsumed by the original demand bound function, then the modification is sustainable. We show an example of how this information can be used in an engineering context where all system parameters are fixed but offsets. We generate all transaction that are subsumed by a schedulable transaction and merge this information in a presentable form for the engineer. This information can be used to safely modify the transaction or to investigate the robustness of the schedulability.
Wheat Straw and Wheat Flour Biocomposites Prepared by Extrusion Process

A study on structural and mechanical properties of bio-composites based on wheat straw and wheat flour is reported with a view to using these low-cost raw materials for the preparation of fully bio-based and biodegradable composites for non-structural applications. The wheat straw was pretreated with sodium hydroxide and fractionated in a twin screw extruder. Chopped straw was also used for comparison purposes. The straw was then extrusion compounded with wheat starch where plasticisation and gelatinisation of the matrix took place. Microstructure and mechanical properties of the compression moulded compounds were examined. The wheat straw formed good adhesion with the matrix which lead to enhanced mechanical properties. Refinement of the straw contributed to the exposure of the straw fibre surfaces. This led to an increase in flexibility and packing efficiency of the straw fibre thus giving a high tensile strength and ductility of the composites. Composites containing untreated chopped straw also displayed comparable mechanical properties and these materials are more cost-competitive alternatives to those containing the refined straw fibre. Copyright © 2010 American Scientific Publishers All rights reserved.
Stress reactivity as a putative mechanism linking childhood trauma with clinical outcomes in individuals at ultra-high-risk for psychosis: Findings from the EU-GEI High Risk Study

Abstract Aims Childhood trauma is associated with an elevated risk for psychosis, but the psychological mechanisms involved remain largely unclear. This study aimed to investigate emotional and psychotic stress reactivity in daily life as a putative mechanism linking childhood trauma and clinical outcomes in individuals at ultra-high-risk (UHR) for psychosis. Methods Experience sampling methodology was used to measure momentary stress, affect and psychotic experiences in the daily life of N = 79 UHR individuals in the EU-GEI High Risk Study. The Childhood Trauma Questionnaire was used to assess self-reported childhood trauma. Clinical outcomes were assessed at baseline, 1- and 2-year follow-up. Results The association of stress with positive (β = −0.14, p = 0.010) and negative affect (β = 0.11, p = 0.020) was modified by transition status such that stress reactivity was greater in individuals who transitioned to psychosis. Moreover, the association of stress with negative affect (β = 0.06, p = 0.019) and psychotic experiences (β = 0.05, p = 0.037) was greater in individuals exposed to high v. low levels of childhood trauma. We also found evidence that decreased positive affect in response to stress was associated with reduced functioning at 1-year follow-up (B = 6.29, p = 0.034). In addition, there was evidence that the association of childhood trauma with poor functional outcomes was mediated by stress reactivity (e.g. indirect effect: B = −2.13, p = 0.026), but no evidence that stress reactivity mediated the association between childhood trauma and transition (e.g. indirect effect: B = 0.14, p = 0.506). Conclusions Emotional and psychotic stress reactivity may be potential mechanisms linking childhood trauma with clinical outcomes in UHR individuals.
Summaries of Doctoral Dissertations

In September 2020, the members of the Economic History Association convened across different time zones and latitudes, for the first (and, one hopes, the final) virtual dissertation session. The last time I had moderated the panel for the Nevins prize was in 2008 when there were a financial crisis and a great recession. This time, there is a financial crisis, a great recession, AND a pandemic. However, I feel secure in the conviction that cliometricians will recognize that correlation does not imply causation. The pandemic of 2020 has disrupted key institutions, overwritten central clauses of the social contract, and heightened concerns about economic inequality and social justice. As Allan Nevins (2018) pointed out, at such times as these, when humans are “harried and perplexed by the sweep of events, [they] peer earnestly into history for some illumination of their predicament and prospects. ” The dissertations under consideration as finalists for the Nevins prize all demonstrate that economic history is more important than ever for understanding vital problems of the present and for its ability to offer insights into more effective ways to attain a just society. SARAH QUINCY completed her thesis as an affiliate of the unparalleled All-UC group in economic history, and this shows. For one, she thanks her advisors at Davis for instruction in the arcane art of (and I quote) “footnote surfing. ” Of course, the EHA does not yet give out prizes for surfing of any kind, but one cannot fail to be impressed by Quincy’s deep-diving into the institutional context and intrepid attempts to get the details right. She crafts the project with artisanal care, making sure that the archival data, statistical tools, and level of aggregation match smoothly without the need for ad hoc econometric patches. The skeptical reader—yes, you will no doubt be surprised to learn that this is my default setting—finds her misgivings assuaged in the very next footnote or table. Society does not seem to follow an evolutionary path of persistent upward progress, but rather one of the fully circular peregrinations. Google searches about the Great Depression have recently soared because the concerns of the 1920s have re-emerged in 2020. Quincy boldly goes where many economists have gone before: her captivating thesis is set in Depression-era California, and she manages to add new facets to this well-burnished topic, in itself a high achievement. Her project explores how creditmarket frictions can constrain household spending, which has implications for resolving the longstanding puzzle in macroeconomics of how changes in nominal variables might have persistent real consequences. In one sentence: she essentially argues that what was good for Bank of America was good for California.1