Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualizing the geography of genetic variants

One of the key characteristics of any genetic variant is its geographic distribution. The geographic distribution can shed light on where an allele first arose, what populations it has spread to, and in turn on how migration, genetic drift, and natural selection have acted. The distribution of a genetic variant can also be of great utility for medical/clinical geneticists. Collectively the geographic distribution of many genetic variants can reveal population structure. As a result, visual inspection of geographic maps for genetic variants is common practice in genetic studies. Here we develop an interactive visualization tool for rapidly displaying the geographic distribution of genetic variants. Through a REST API and dynamic front-end the Geography of Genetic Variants (GGV) browser provides maps of allele frequencies in populations distributed across the globe.
Assessment of Blood Lead Levels Among Children Aged ≤5 Years — Zamfara State, Nigeria, June–July 2012

Since 2010, Nigerian state and federal governments and the international community have been responding to an outbreak of lead poisoning caused by the processing of lead-containing gold ore in Zamfara State, Nigeria, that resulted in the deaths of approximately 400 children aged ≤ 5 years. Widespread education, surveys of high-risk villages, testing of blood lead levels (BLLs), medical treatment, and environmental cleanup all have been implemented. To evaluate the success of these remediation efforts in reducing the prevalence of lead poisoning and dangerous work practices, a population-based assessment of children's BLLs and ore processing techniques was conducted during June-July 2012. The assessment found few children in need of medical treatment, significantly lower BLLs, and substantially less exposure of children to dangerous work practices. Public health strategies designed to identify and treat children with lead poisoning, clean up existing environmental hazards, and prevent children from being exposed to dangerous ore processing techniques can produce a sustained reduction in BLLs.
Effects of Aerobic Exercise on Cognitive Performance Among Young Adults in a Higher Education Setting

ABSTRACT Purpose: Acute benefits of aerobic exercise on executive functioning have been reported frequently under laboratory conditions. However, to date, a beneficial effect on long-term memory has been less well supported and no data are available regarding nonlaboratory conditions in young adults. The aim of the current study was to investigate acute effects of aerobic exercise on cognitive functioning in a university classroom setting. Method: Using a cross-over design, 51 participants performed a bout of moderately intense running (RUN) and read an article while seated (CON). Afterwards, they completed free-recall tests, followed by a Flanker task and an n-back task. Results: Participants in the RUN condition compared with those in the CON condition showed shorter reaction time on the inhibition task, F(1, 50) = 5.59, p = . 022, η2 = . 101, and recalled more words in the immediate- and delayed-recall tests, F(1, 50) = 8.40, p = . 006, η2 = . 144. Conclusion: The present findings suggest that a moderately intense bout of aerobic exercise benefits verbal short-term and long-term memory as well as inhibitory control among students in a classroom setting.
An Essential Role for Medullary Thymic Epithelial Cells during the Intrathymic Development of Invariant NKT Cells

In the thymus, interactions with both cortical and medullary microenvironments regulate the development of self-tolerant conventional CD4+ and CD8+ αβT cells expressing a wide range of αβTCR specificities. Additionally, the cortex is also required for the development of invariant NKT (iNKT) cells, a specialized subset of T cells that expresses a restricted αβTCR repertoire and is linked to the regulation of innate and adaptive immune responses. Although the role of the cortex in this process is to enable recognition of CD1d molecules expressed by CD4+CD8+ thymocyte precursors, the requirements for additional thymus microenvironments during iNKT cell development are unknown. In this study, we reveal a role for medullary thymic epithelial cells (mTECs) during iNKT cell development in the mouse thymus. This requirement for mTECs correlates with their expression of genes required for IL-15 trans-presentation, and we show that soluble IL-15/IL-15Rα complexes restore iNKT cell development in the absence of mTECs. Furthermore, mTEC development is abnormal in iNKT cell–deficient mice, and early stages in iNKT cell development trigger receptor activator for NF-κB ligand–mediated mTEC development. Collectively, our findings demonstrate that intrathymic iNKT cell development requires stepwise interactions with both the cortex and the medulla, emphasizing the importance of thymus compartmentalization in the generation of both diverse and invariant αβT cells. Moreover, the identification of a novel requirement for iNKT cells in thymus medulla development further highlights the role of both innate and adaptive immune cells in thymus medulla formation.
Use of a Social Annotation Platform for Pre-Class Reading Assignments in a Flipped Introductory Physics Class

In this paper, we illustrate the successful implementation of pre-class reading assignments through a social learning platform that allows students to discuss the reading online with their classmates. We show how the platform can be used to understand how students are reading before class. We find that, with this platform, students spend an above average amount of time reading (compared to that reported in the literature) and that most students complete their reading assignments before class. We identify specific reading behaviors that are predictive of in-class exam performance. We also demonstrate ways that the platform promotes active reading strategies and produces high-quality learning interactions between students outside class. Finally, we compare the exam performance of two cohorts of students, where the only difference between them is the use of the platform; we show that students do significantly better on exams when using the platform.
Physiological and Molecular Effects of in vivo and ex vivo Mild Skin Barrier Disruption

The success of topically applied treatments on skin relies on the efficacy of skin penetration. In order to increase particle or product penetration, mild skin barrier disruption methods can be used. We previously described cyanoacrylate skin surface stripping as an efficient method to open hair follicles, enhance particle penetration, and activate Langerhans cells. We conducted ex vivo and in vivo measurements on human skin to characterize the biological effect and quantify barrier disruption-related inflammation on a molecular level. Despite the known immunostimulatory effects, this barrier disruption and hair follicle opening method was well accepted and did not result in lasting changes of skin physiological parameters, cytokine production, or clinical side effects. Only in ex vivo human skin did we find a discrete increase in IP-10, TGF-β, IL-8, and GM-CSF mRNA. The data underline the safety profile of this method and demonstrate that the procedure per se does not cause substantial inflammation or skin damage, which is also of interest when applied to non-invasive sampling of biomarkers in clinical trials.
How Effectively Do People Remember Voice Disordered Speech? An Investigation of the Serial-Position Curve

We examined how well typical adult listeners remember the speech of a person with a voice disorder (relative to that of a person without a voice disorder). Participants (n = 40) listened to two lists of words (one list uttered in a disordered voice and the other list uttered in a normal voice). After each list, participants completed a free recall test, in which they tried to remember as many words as they could. While the total number of words recalled did not differ between the disordered voice condition and the normal voice condition, an investigation of the serial-position curve revealed a difference. In the normal voice condition, a parabolic (i.e., u-shaped) serial-position curve was observed, with a significant primacy effect (i.e., the beginning of the list was remembered better than the middle) and a significant recency effect (i.e., the end of the list was remembered better than the middle). In contrast, in the disordered voice condition, while there was a significant recency effect, no primacy effect was present. Thus, the increased ability to remember the first words uttered by a speaker (relative to subsequent words) may disappear when the speaker has a voice disorder. Explanations and implications of this finding are discussed.
User needs analysis and usability assessment of DataMed – a biomedical data discovery index

Abstract Objective To present user needs and usability evaluations of DataMed, a Data Discovery Index (DDI) that allows searching for biomedical data from multiple sources. Materials and Methods We conducted 2 phases of user studies. Phase 1 was a user needs analysis conducted before the development of DataMed, consisting of interviews with researchers. Phase 2 involved iterative usability evaluations of DataMed prototypes. We analyzed data qualitatively to document researchers’ information and user interface needs. Results Biomedical researchers’ information needs in data discovery are complex, multidimensional, and shaped by their context, domain knowledge, and technical experience. User needs analyses validate the need for a DDI, while usability evaluations of DataMed show that even though aggregating metadata into a common search engine and applying traditional information retrieval tools are promising first steps, there remain challenges for DataMed due to incomplete metadata and the complexity of data discovery. Discussion Biomedical data poses distinct problems for search when compared to websites or publications. Making data available is not enough to facilitate biomedical data discovery: new retrieval techniques and user interfaces are necessary for dataset exploration. Consistent, complete, and high-quality metadata are vital to enable this process. Conclusion While available data and researchers’ information needs are complex and heterogeneous, a successful DDI must meet those needs and fit into the processes of biomedical researchers. Research directions include formalizing researchers’ information needs, standardizing overviews of data to facilitate relevance judgments, implementing user interfaces for concept-based searching, and developing evaluation methods for open-ended discovery systems such as DDIs.
Sclerotherapy for the Treatment of Gastric Antral Vascular Ectasia in Case of Contraindications to Argon

Gastric antral vascular ectasia (GAVE) is a rare cause of chronic gastro-intestinal hemorrhage. GAVE can be observed in patients with cirrhosis and it is involved in several cases of persistent anemia, sometimes requiring blood transfusions due to the severity of anemia. Argon Plasma Coagulation (APC) has been proven to be effective and safe in the treatment of GAVE, the only contraindications being the presence of a pacemaker or defibrillator, susceptibility to electrical interference. We here report the case of a patient bleeding from GAVE with contraindications to use of APC. In this patient sclerotherapy with Polidocanol proved to be safe and effective endoscopic procedure, representing a potential alternative to Endoscopic Band Ligation (EBL).
Assessing the Network of Agencies in Local Communities that Promote Healthy Eating and Lifestyles among Populations with Limited Resources.

OBJECTIVES We assessed the network of agencies in local communities that promote healthy eating and lifestyles among populations with limited resources. METHODS Network surveys were administered among 159 Illinois agencies identified as serving limited-resource audiences categorized into 8 types: K-12 schools, early childhood centers, emergency food providers, health-related agencies, social resource centers, low-income/subsidized housing complexes, continuing education organizations, and others. Network analysis was conducted to examine 4 network structures - communications, funding, cooperation, and collaboration networks between agencies within each county/county cluster. RESULTS Agencies in a network were found to be loosely connected, indicated by low network density. Reporting accuracy might be of concern, indicated by low reciprocity. Agencies in a network are decentralized rather than centralized around a few influential agencies, indicated by low betweenness centrality. There is suggestive evidence regarding homophily in a network, indicated by some significant correlations within agencies of the same type. Agencies connected in one network are significantly more likely to be connected in all the other networks as well. CONCLUSIONS Promoting healthy eating and lifestyles among populations with limited resources warrants strong partnership across agencies in communities. Network analysis serves as a useful tool to evaluate community partnerships and facilitate coalition building.
A Case Study on the Communication and Computation Behaviors of Real Applications in NoC-Based MPSoCs

Network-on-chip (NoC) based multiprocessor system-on-chips (MPSoCs) have been proposed as promising architectures to meet modern applications' ever-increasing demands for computing capability under limited power budget. Understanding the behaviors of MPSoC applications is the key to design MPSoCs under tight power and performance constraints. In this case study, we systematically examine the computation and communication behaviors of four real applications on MPSoCs based on three popular NoC topologies. We formally model real multiprocessor applications as task communication graphs (TCG) to accurately capture their computation and communication requirements. We publicly release a multiprocessor benchmark suite called COSMIC online, which includes the TCG models. In this work, we analyze the spatial distributions of workloads and traffics for each application, and evaluate their performance and energy efficiency on various MPSoC architectures. Our study shows that fat tree based MPSoCs are good choices for applications requiring high network throughput.
ACR appropriateness criteria® nasal cavity and paranasal sinus cancers

The American College of Radiology (ACR) Appropriateness Criteria are evidence‐based guidelines for specific clinical conditions that are reviewed annually by a multidisciplinary expert panel. The guideline development and revision include an extensive analysis of current medical literature from peer‐reviewed journals and the application of well‐established methodologies (RAND/UCLA Appropriateness Method and Grading of Recommendations Assessment, Development, and Evaluation or GRADE) to rate the appropriateness of imaging and treatment procedures for specific clinical scenarios. In those instances where evidence is lacking or equivocal, expert opinion may supplement the available evidence to recommend imaging or treatment. Here, we present the Appropriateness Criteria for cancers arising in the nasal cavity and paranasal sinuses (maxillary, sphenoid, and ethmoid sinuses). This includes clinical presentation, prognostic factors, principles of management, and treatment outcomes. Controversies regarding management of cervical lymph nodes are discussed. Rare and unusual nasal cavity cancers, such as esthesioneuroblastoma and sinonasal undifferentiated carcinomas, are included. © 2016 American College of Radiology. Head Neck, 2016 © 2016 Wiley Periodicals, Inc. Head Neck 39: 407–418, 2017
Abdominal radical trachelectomy guided by sentinel lymph node biopsy for stage IB1 cervical cancer with tumors >2 cm

Accuracy of prediction of pelvic lymph node status using sentinel lymph node biopsy (SLNB), and outcomes of SLNB-guided abdominal radical trachelectomy (ART) were assessed. Patients with stage IB1 (Figure 2009) cervical cancer and with tumors >2 cm were enrolled. Prior to fertility-sparing surgery 99mTc-labeled phytate was administered. SLNs were intraoperatively identified, excised, and assessed using fast-frozen sections. Systematic bilateral pelvic lymphadenectomy with or without para-aortic lymphadenectomy was subsequently undertaken. The SLN detection rate was 91.8% (45/49 patients); 8.2% (4/49) had radical hysterectomies because of metastatic primary SLNs. All SLNs received routine immunopathological examination to detect micrometastasis. Sensitivity, accuracy, and false negative rates were 100%, 100%, and 0%, respectively. ART was successfully completed in 45 patients (median follow-up, 61 [range, 4–149] months). Three of the 45 (6.7%) were lost to follow-up; two relapsed and one died of tumor progression. Overall 3-year survival and progression-free survival rates were 97.6% and 95.2%, respectively. Of the 19 patients who attempted to conceive after surgery, five achieved pregnancy, and one had a live birth in the third trimester. We concluded that SLNB using 99mTc-labeled phytate can accurately assess pelvic node status. SLNB-guided ART is safe and feasible in patients selected for fertility-sparing procedures.
Redox properties of birnessite from a defect perspective

Significance We propose, and preliminarily confirm with experiments, a theoretical model to understand various structure–performance dependences of layered-structure birnessite as an oxygen evolution reaction (OER) catalyst. Besides the well-accepted importance of Mn(III), we emphasize the critical importance of a nonuniform distribution of Mn(III) to OER catalytic activity. Such a distribution contributes to the reduction of the overpotential by building an internal potential step. We further propose the small polaron as a common concept to link the fields of oxygen evolution catalysis and Li-ion batteries, suggesting a promising candidate space for oxygen evolution reaction catalysts. Birnessite, a layered-structure MnO2, is an earth-abundant functional material with potential for various energy and environmental applications, such as water oxidation. An important feature of birnessite is the existence of Mn(III) within the MnO2 layers, accompanied by interlayer charge-neutralizing cations. Using first-principles calculations, we reveal the nature of Mn(III) in birnessite with the concept of the small polaron, a special kind of point defect. Further taking into account the effect of the spatial distribution of Mn(III), we propose a theoretical model to explain the structure–performance dependence of birnessite as an oxygen evolution catalyst. We find an internal potential step which leads to the easy switching of the oxidation state between Mn(III) and Mn(IV) that is critical for enhancing the catalytic activity of birnessite. Finally, we conduct a series of comparative experiments which support our model.
Interventions to prevent or reduce the level of frailty in community-dwelling older adults: a scoping review of the literature and international policies

Abstract Background frailty impacts older adults’ ability to recover from an acute illness, injuries and other stresses. Currently, a systematic synthesis of available interventions to prevent or reduce frailty does not exist. Therefore, we conducted a scoping review of interventions and international policies designed to prevent or reduce the level of frailty in community-dwelling older adults. Methods and analysis we conducted a scoping review using the framework of Arksey and O'Malley. We systematically searched articles and grey literature to identify interventions and policies that aimed to prevent or reduce the level of frailty. Results fourteen studies were included: 12 randomised controlled trials and 2 cohort studies (mean number of participants 260 (range 51–610)), with most research conducted in USA and Japan. The study quality was moderate to good. The interventions included physical activity; physical activity combined with nutrition; physical activity plus nutrition plus memory training; home modifications; prehabilitation (physical therapy plus exercise plus home modifications) and comprehensive geriatric assessment (CGA). Our review showed that the interventions that significantly reduced the number of frailty markers present or the prevalence of frailty included the physical activity interventions (all types and combinations), and prehabilitation. The CGA studies had mixed findings. Conclusion nine of the 14 studies reported that the intervention reduced the level of frailty. The results need to be interpreted with caution, as only 14 studies using 6 different definitions of frailty were retained. Future research could combine interventions targeting more frailty markers including cognitive or psychosocial well-being.
Genomic analysis of induced pluripotent stem (iPS) cells: routes to reprogramming

The phenomenal proliferation of scientific studies into the nature of induced pluripotent stem (iPS) cells following publication of the findings of Takahashi and Yamanaka little more than 2 years ago, have significantly expanded our understanding of cellular mechanisms relating to cell lineage, differentiation, and proliferation. While the full potential of iPS cell lineages for both scientific tool and therapeutic applications is as yet unclear, findings from several lines of investigation suggests that multipotential and terminally differentiated cells from an array of cell types are competent to undergo epigenetic reprogramming to a pluripotential state. The nature of this pluripotential state appears to be similar to, but not identical with that previously described for embryonic stem (ES) cells. Understanding the nature of this induced reprogrammed state will be critical to determining the full potential of iPS cells. Recently, this issue has been examined through an integrated analysis of the genome in fully and partially reprogrammed iPS cell lineages. These results provide a window onto the temporal components of reprogramming and suggest mechanisms by which the efficacy of reprogramming can be enhanced.
A large dynamic‐range, high dB‐linearity VGA using switch arrays and second‐order mismatch‐shaping DEM technique

A new large dynamic‐range variable gain amplifier (VGA) with improved dB linearity is presented. The traditional cascade VGA has the disadvantages of gain mismatch between sub‐stages and difficulty of employing mismatch cancelation or suppression algorithms. In this paper, switch arrays were used to make the sub‐stages or called gain cells in the coarse‐tuning stage (CTS) work independently and therefore prevent the integral operation of the gain errors. Then, a second‐order mismatch‐shaping DEM was applied conveniently to the CTS and shown to be a useful design technique in improving the dB‐linearity performance. The cascade VGA and its second‐order mismatch‐shaping DEM had been integrated in a 2.4‐GHz receiver chip which was fabricated in a 0.18‐µm CMOS technology with a supply voltage of 1.8 V. Measurement results showed that the gain errors were significantly reduced with second‐order mismatch‐shaping DEM with respect to the traditionally thermometric decoding over a temperature range of [−40, 80] °C. Copyright © 2015 John Wiley & Sons, Ltd.