Miracle-dz/UniFAR-FTUs huggingface dataset:
Murine intestinal organoids resemble intestinal epithelium in their microRNA profiles

Abstract Intestinal organoids were established as an ex vivo model of the intestinal epithelium. We investigated whether organoids resemble the intestinal epithelium in their microRNA (miRNA) profiles. Total RNA samples were obtained from crypt and villus fractions in murine intestine and from cultured organoids. Microarray analysis showed that organoids largely resembled intestinal epithelial cells in their miRNA profiles. In silico prediction followed by qRT-PCR suggested that six genes are regulated by corresponding miRNAs along the crypt-villus axis, suggesting miRNA regulation of epithelial cell renewal in the intestine. However, such expression patterns of miRNAs and their target mRNAs were not reproduced during organoids maturation. This might be due to lack of luminal factors and endocrine, nervous, and immune systems in organoids and different cell populations between in vivo epithelium and organoids. Nevertheless, we propose that intestinal organoids provide a useful in vitro model to investigate miRNA expression in intestinal epithelial cells.
Prospective analysis of radiation oncology image and plan‐driven peer review for head and neck cancer

Departmental “chart rounds” is an established form of review in radiation oncology, however, evidence is lacking that identifies links between features of a more subspecialized disease site‐specific review and the likelihood and characteristics of recommendations made. We prospectively analyzed our head and neck group's review process to identify associations that could guide future practice.
Manifold learning for dimensionality reduction and clustering of skin spectroscopy data

Diagnosis of benign and malign skin lesions is currently done mostly relying on visual assessment and frequent biopsies performed by dermatologists. As the timely and correct diagnosis of these skin lesions is one of the most important factors in the therapeutic outcome, leveraging new technologies to assist the dermatologist seems natural. Optical spectroscopy is a technology that is being established to aid skin lesion diagnosis, as the multi-spectral nature of this imaging method allows to detect multiple physiological changes like those associated with increased vasculature, cellular structure, oxygen consumption or edema in tumors. However, spectroscopy data is typically very high dimensional (on the order of thousands), which causes difficulties in visualization and classification. In this work we apply different manifold learning techniques to reduce the dimensions of the input data and get clustering results. Spectroscopic data of 48 patients with suspicious and actually malignant lesions was analyzed using ISOMAP, Laplacian Eigenmaps and Diffusion Maps with varying parameters and compared to results using PCA. Using optimal parameters, both ISOMAP and Laplacian Eigenmaps could cluster the data into suspicious and malignant with 96% accuracy, compared to the diagnosis of the treating physicians.
Measuring metabolic rate in the field: the pros and cons of the doubly labelled water and heart rate methods

Summary 1Measuring the metabolic rate of animals in the field (FMR) is central to the work of ecologists in many disciplines. In this article we discuss the pros and cons of the two most commonly used methods for measuring FMR. 2Both methods are constantly under development, but at the present time can only accurately be used to estimate the mean rate of energy expenditure of groups of animals. The doubly labelled water method (DLW) uses stable isotopes of hydrogen and oxygen to trace the flow of water and carbon dioxide through the body over time. From these data, it is possible to derive a single estimate of the rate of oxygen consumption () for the duration of the experiment. The duration of the experiment will depend on the rate of flow of isotopes of oxygen and hydrogen through the body, which in turn depends on the animal's size, ranging from 24 h for small vertebrates to up to 28 days in Humans. 3This technique has been used widely, partly as a result of its relative simplicity and potential low cost, though there is some uncertainty over the determination of the standard error of the estimate of mean . 4The heart rate (fH) method depends on the physiological relationship between heart rate and . 5If these two quantities are calibrated against each other under controlled conditions, fH can then be measured in free-ranging animals and used to estimate . 6The latest generation of small implantable data loggers means that it is possible to measure fH for over a year on a very fine temporal scale, though the current size of the data loggers limits the size of experimental animals to around 1 kg. However, externally mounted radio-transmitters are now sufficiently small to be used with animals of less than 40 g body mass. This technique is gaining in popularity owing to its high accuracy and versatility, though the logistic constraint of performing calibrations can make its use a relatively extended process.
Evaluating the Impact of Trauma-Informed Care (TIC) Perspective in Social Work Curriculum

Abstract A trauma-informed care (TIC) curriculum was integrated into a school of social work master’s level program. Measures assessed the impact of the curriculum on first and advanced-year students’ knowledge, attitude, self-efficacy, and behavioral intention at the beginning and end of a semester. Initial comparisons show advanced-year students as having more knowledge about TIC, more positive attitudes toward TIC, higher levels of self-efficacy to use TIC approaches, and greater likelihood to engage in TIC behaviors than first-year students. However, by the end of the semester, the latter were equivalent with advanced students on all measures. Results suggest the first-year curriculum provides sufficient background in TIC approaches to allow for significant gains across all areas assessed. However, integration of the TIC perspective within advanced courses needs further assessment.
Comparison of brain areas for executed and imagined movements after motor training: An fNIRS study

In this paper, we investigate active brain regions for motor execution and motor imagination tasks after training with a rehabilitation robot. Functional near-infrared spectroscopy (fNIRS) is used to measure the hemodynamic responses in the motor cortices of five subjects. An assistive robot (IMT 2.0, connected to the right hand) is used during the training session to make the subject to reach a target point displayed on a computer screen. During the training, the subjects have to reach the target point in two directions (left and right) using right arm movement. Our intention is to investigate the differences between brain signals generated from left and right movements of the right hand. It was found that the same brain region was activated for both left- and right-directional motions. During the testing, we asked the subjects to imagine the executed movement. We found that although the imagined movement activity is weak but it appears in the same region as that of motor execution during the reach task. The results show that executed and imagined movements can be discriminated using fNIRS. However, for brain-computer interface it is difficult to generate two commands using only one arm movement signals.
Tight Bounds for Undirected Graph Exploration with Pebbles and Multiple Agents

We study the problem of deterministically exploring an undirected and initially unknown graph with n vertices either by a single agent equipped with a set of pebbles or by a set of collaborating agents. The vertices of the graph are unlabeled and cannot be distinguished by the agents, but the edges incident to a vertex have locally distinct labels. The graph is explored when all vertices have been visited by at least one agent. In this setting, it is known that for a single agent without pebbles Θ(log n) bits of memory are necessary and sufficient to explore any graph with at most n vertices. We are interested in how the memory requirement decreases as the agent may mark vertices by dropping and retrieving distinguishable pebbles or when multiple agents jointly explore the graph. We give tight results for both questions showing that for a single agent with constant memory Θ(log log n) pebbles are necessary and sufficient for exploration. We further prove that using collaborating agents instead of pebbles does not help as Θ(log log n) agents with constant memory each are necessary and sufficient for exploration. For the upper bounds, we devise an algorithm for a single agent with constant memory that explores any n-vertex graph using O(log log n) pebbles, even when n is not known a priori. The algorithm terminates after polynomial time and returns to the starting vertex. We further show that the algorithm can be realized with additional constant-memory agents rather than pebbles, implying that O(log log n) agents with constant memory can explore any n-vertex graph. For the lower bound, we show that the number of agents needed for exploring any graph with at most n vertices is already Ω(log log n) when we allow each agent to have at most O((log n)1-ε) bits of memory for any ε > 0. Our argument also implies that a single agent with sublogarithmic memory needs Θ(log log n) pebbles to explore any n-vertex graph.
Energy efficient communication in smart building WSN running distributed Hidden Markov chain presence detection algorithm

Occupancy detection in smart buildings suffers from high sensor unreliability. The combination of data from multiple sensors can largely improve reliability. However, battery-powered sensor nodes have communication limitations. This paper addresses the problem of presence detection in a building as Distributed Sensing of a Hidden Markov Model (DS-HMM). Optimal solutions require excessive communication over a perfectly reliable channel. We propose and investigate an efficient transmission policy, jointly with a fusion algorithm, to merge data from various HMMs running separately on all sensor nodes. The algorithm showed improved performance and potential energy savings in a real world set-up, where user presence and sensor errors may not exactly follow idealized model assumptions.
Highly Scalable Image Reconstruction using Deep Neural Networks with Bandpass Filtering

To increase the flexibility and scalability of deep neural networks for image reconstruction, a framework is proposed based on bandpass filtering. For many applications, sensing measurements are performed indirectly. For example, in magnetic resonance imaging, data are sampled in the frequency domain. The introduction of bandpass filtering enables leveraging known imaging physics while ensuring that the final reconstruction is consistent with actual measurements to maintain reconstruction accuracy. We demonstrate this flexible architecture for reconstructing subsampled datasets of MRI scans. The resulting high subsampling rates increase the speed of MRI acquisitions and enable the visualization rapid hemodynamics.
GUI generation from annotated source code

Creating user interfaces in a common task in application development. It can become time and money consuming if the same application is to be run on more platforms with different restrictions and requirements. To reduce the development cost and time the user interface can be defined on an abstract level in the form of a task model. Explicit defining and maintaining the task model can complicate the development especially in its early stages when application prototype are built. We present a way to define a user interface on an abstract level without explicit definition of the user interface module while keeping it transparent, thus reducing the work required to make functional application prototypes. Our approach is based on derivation of a user interface module directly from an application source code enriched by abstract commands of user interaction to control the generation of the user interface.
“Harden Up and Face Reality:” Exploring Underlying Bullying Beliefs in New Zealand

ABSTRACT A growing body of research illustrating the detrimental consequences of bullying has led to many antibullying interventions being developed. Despite good intentions, evidence suggests that such programs vary considerably in their efficacy. The current study examines the social discourse around bullying in the New Zealand environment in order to see whether underlying beliefs may undermine or influence approaches to mitigate bullying. The study employed an exploratory, qualitative approach of social discourses in the media. Using 31 online media articles, and 501 related online comments, methods of applied thematic analysis revealed three main themes which captured the beliefs that (a) victims of bullying are weak, (b) perpetrators of bullying are evil, and (c) bullying is a normal and, in some ways, acceptable behavior. Such findings illustrate the role that societal beliefs play in shaping the environment in which bullying occurs, and have important implications for future bullying research and interventions.
High mobility group A2 (HMGA2) deficiency in pigs leads to dwarfism, abnormal fetal resource allocation, and cryptorchidism

Significance We show that mutations in HMGA2 affect fetal resource allocation, testis descent, and the size of pigs and provides a target for gene modification that can be used to modulate size in other mammalian species. This can have implications in agriculture as well as in the development of new strains of companion animals. In addition, most xenograft pig donors have adult organs larger than those of humans. Recently, it has been shown that regulation of organ growth is donor-controlled, not host-controlled, resulting in organ overgrowth and damage after transplantation. We show here that the HMGA2 gene is a potential target for organ-size regulation in xenotransplantation. Expression of HMGA2 is strongly associated with body size and growth in mice and humans. In mice, inactivation of one or both alleles of Hmga2 results in body-size reductions of 20% and 60%, respectively. In humans, microdeletions involving the HMGA2 locus result in short stature, suggesting the function of the HMGA2 protein is conserved among mammals. To test this hypothesis, we generated HMGA2-deficient pigs via gene editing and somatic cell nuclear transfer (SCNT). Examination of growth parameters revealed that HMGA2−/+ male and female pigs were on average 20% lighter and smaller than HMGA2+/+ matched controls (P < 0.05). HMGA2−/− boars showed significant size reduction ranging from 35 to 85% of controls depending on age (P < 0.05), and organ weights were also affected (P < 0.05). HMGA2−/+ gilts and boars exhibited normal reproductive development and fertility, while HMGA2−/− boars were sterile due to undescended testes (cryptorchidism). Crossbreeding HMGA2−/+ boars and gilts produced litters lacking the HMGA2−/− genotype. However, analysis of day (D) D40 and D78 pregnancies indicated that HMGA2−/− fetuses were present at the expected Mendelian ratio, but placental abnormalities were seen in the D78 HMGA2−/− concepti. Additionally, HMGA2−/− embryos generated by gene editing and SCNT produced multiple pregnancies and viable offspring, indicating that lack of HMGA2 is not lethal per se. Overall, our results show that the effect of HMGA2 with respect to growth regulation is highly conserved among mammals and opens up the possibility of regulating body and organ size in a variety of mammalian species including food and companion animals.
Training Corpus Preprocessing Sentence Preprocessing BEL Statement Preprocessing NER and Mapping Parallel Corpus Construction Named Entity Source Sentence Construction Training Corpus Generation Word Alignment Hierarchically Tagged Corpus Generation Hierarchically Tagged Corpus Target Sequence

We implemented a hierarchical sequence labeling system for BioCreative VI Track 3 BEL Task 1—extract BEL statements from sentences with or without gold entity annotations. Different from previous systems for BEL task, we mapped sentence-level BEL statements in the BCV 2015 training corpus to the corresponding text segments, thus generating hierarchically tagged training sentences. A hierarchical sequence labeling model was afterwards induced from the training sentences and applied to the test sentences in order to construct the BEL statements. The system achieved an overall F-measure of 22.66% and 10.67% respectively for the test sentences with or without gold entity annotation. The potential of our system is that many advanced machine learning methods can be adopted in the future to further enhance the BEL extraction system. Keywords—Biological Expression Language; Dependency Parsing; Alignment Algorithm; Hierarchical Sequence Labeling
SOVA: Design of a Stakeholder Informed Social Media Website for Depressed Adolescents and Their Parents

ABSTRACT Two moderated social media websites were designed for increasing likelihood for mental health treatment engagement for depressed adolescents (sova.pitt.edu) and for parents (wisesova.pitt.edu). This article describes iterative stakeholder interviews conducted with adolescents, young adults, parents, advocates, and clinicians and use of human computer interaction techniques to inform major design changes which: (a) underscored the role of online interaction to provide emotional support and information, (b) importance of anonymity, (c) desire to share positive media, and (d) need for frequent moderation. Future studies will examine acceptability and effectiveness of revised websites in helping depressed adolescents and their parents engage with treatment.
Neural Cache: Bit-Serial In-Cache Acceleration of Deep Neural Networks

This paper presents the Neural Cache architecture, which re-purposes cache structures to transform them into massively parallel compute units capable of running inferences for Deep Neural Networks. Techniques to do in-situ arithmetic in SRAM arrays, create efficient data mapping and reducing data movement are proposed. The Neural Cache architecture is capable of fully executing convolutional, fully connected, and pooling layers in-cache. The proposed architecture also supports quantization in-cache. Our experimental results show that the proposed architecture can improve inference latency by 8.3× over state-of-art multi-core CPU (Xeon E5), 7.7× over server class GPU (Titan Xp), for Inception v3 model. Neural Cache improves inference throughput by 12.4× over CPU (2.2× over GPU), while reducing power consumption by 50% over CPU (53% over GPU).
The global education practicum: perspectives from accompanying academics

ABSTRACT The benefits of international education experiences for students are well documented. The effect on the individual of international experiences has been researched and theorised by authors for at least the last 20 years. In this paper the experiences of three academics who accompanied pre-service teachers on a 3 week international practicum are examined through the prism of intercultural confidence and competence. Accompanying academic Juliet reflects on dealing with the added difficulties the pre-service teachers encountered as a result of their inexperience in classroom settings. Accompanying academic Paula reflects on the challenges of “teaching-out-of-field. ” Accompanying academic Sue reflects on the social and transitional challenges experienced when supporting pre-service teachers who collectively had issues related to health, safety, and interpersonal relationships. These lived experiences provide a richer understanding of the role of international partnerships in contributing to academic growth and increasing intercultural competency in tandem with their students.
Optoelectronic Performance Variations in InGaN/GaN Multiple-Quantum-Well Light-Emitting Diodes: Effects of Potential Fluctuation

We investigate the cause of the optoelectronic performance variations in InGaN/GaN multiple-quantum-well blue light-emitting diodes, using three different samples from an identical wafer grown on a c-plane sapphire substrate. Various macroscopic measurements have been conducted, revealing that with increasing strain in the quantum wells (QWs), the crystal quality improves with an increasing peak internal quantum efficiency while the droop becomes more severe. We propose to explain these variations using a model where the in-plane local potential fluctuation in QWs is considered. Our work is contrasted with prior works in that macroscopic measurements are utilized to find clues on the microscopic changes and their impacts on the device performances, which has been rarely attempted.
Common and Distinct Capsid and Surface Protein Requirements for Secretion of Complete and Genome-Free Hepatitis B Virions

ABSTRACT During the morphogenesis of hepatitis B virus (HBV), an enveloped virus, two types of virions are secreted: (i) a minor population of complete virions containing a mature nucleocapsid with the characteristic, partially double-stranded, relaxed circular DNA genome and (ii) a major population containing an empty capsid with no DNA or RNA (empty virions). Secretion of both types of virions requires interactions between the HBV capsid or core protein (HBc) and the viral surface or envelope proteins. We have studied the requirements from both HBc and envelope proteins for empty virion secretion in comparison with those for secretion of complete virions. Substitutions within the N-terminal domain of HBc that block secretion of DNA-containing virions reduced but did not prevent secretion of empty virions. The HBc C-terminal domain was not essential for empty virion secretion. Among the three viral envelope proteins, the smallest, S, alone was sufficient for empty virion secretion at a basal level. The largest protein, L, essential for complete virion secretion, was not required but could stimulate empty virion secretion. Also, substitutions in L that eliminated secretion of complete virions reduced but did not eliminate empty virion secretion. S mutations that blocked secretion of the hepatitis D virus (HDV), an HBV satellite, did not block secretion of either empty or complete HBV virions. Together, these results indicate that both common and distinct signals on empty capsids and mature nucleocapsids interact with the S and L proteins during the formation of complete and empty virions. IMPORTANCE Hepatitis B virus (HBV) is a major cause of severe liver diseases, including cirrhosis and cancer. In addition to the complete infectious virion particle, which contains an outer envelope layer and an interior capsid that, in turn, encloses a DNA genome, HBV-infected cells also secrete noninfectious, incomplete viral particles in large excess over the number of complete virions. In particular, the empty (or genome-free) virion shares with the complete virion the outer envelope and interior capsid but contains no genome. We have carried out a comparative study on the capsid and envelope requirements for the secretion of these two types of virion particles and uncovered both shared and distinct determinants on the capsid and envelope for their secretion. These results provide new information on HBV morphogenesis and have implications for efforts to develop empty HBV virions as novel biomarkers and a new generation of HBV vaccine.