Miracle-dz/UniFAR-FTUs huggingface dataset:
Histopathology findings of non-mass cancers on breast ultrasound

Background There is little research done on non-mass cancers (NMCs) on breast ultrasound (US). Purpose To evaluate large-sectional histopathology findings of NMCs on breast US. Material and Methods The mammographic and histopathology features of biopsy proven 36 breast cancers which showed pure non-mass lesions on US were retrospectively reviewed. Results The most common mammographic finding was microcalcification (23/35, 65.7%); fine pleomorphic microcalcification was predominant (18/23, 78.3%). The main tumor type was pure ductal carcinoma in situ (DCIS) (14/36, 38.9%) and DCIS with micro- or minimal invasion (11/36, 30.6%). Among the 25 DCIS, histologic grade was high in 15 (60.0%) and intermediate in nine (36%); comedo necrosis was seen in 17 (68%). Immunohistochemical analysis was available in 27 lesions and showed HER2-overexpression in 12 (44.4%) and triple-negative in two (7.4%). Conclusion According to our limited patient sample, NMCs on breast US were mainly associated with high-grade DCIS.
Temozolomide lymphodepletion enhances CAR abundance and correlates with antitumor efficacy against established glioblastoma

ABSTRACT Adoptive transfer of T cells expressing chimeric antigen receptors (CARs) is an effective immunotherapy for B-cell malignancies but has failed in some solid tumors clinically. Intracerebral tumors may pose challenges that are even more significant. In order to devise a treatment strategy for patients with glioblastoma (GBM), we evaluated CARs as a monotherapy in a murine model of GBM. CARs exhibited poor expansion and survival in circulation and failed to treat syngeneic and orthotopic gliomas. We hypothesized that CAR engraftment would benefit from host lymphodepletion prior to immunotherapy and that this might be achievable by using temozolomide (TMZ), which is standard treatment for these patients and has lymphopenia as its major side effect. We modelled standard of care temozolomide (TMZSD) and dose-intensified TMZ (TMZDI) in our murine model. Both regimens are clinically approved and provide similar efficacy. Only TMZDI pretreatment prompted dramatic CAR proliferation and enhanced persistence in circulation compared to treatment with CARs alone or TMZSD + CARs. Bioluminescent imaging revealed that TMZDI + CARs induced complete regression of 21-day established brain tumors, which correlated with CAR abundance in circulation. Accordingly, TMZDI + CARs significantly prolonged survival and led to long-term survivors. These findings are highly consequential, as it suggests that GBM patients may require TMZDI as first line chemotherapy prior to systemic CAR infusion to promote CAR engraftment and antitumor efficacy. On this basis, we have initiated a phase I trial in patients with newly diagnosed GBM incorporating TMZDI as a preconditioning regimen prior to CAR immunotherapy (NCT02664363).
Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential

Phasing of nucleic acid crystal diffraction data using the anomalous signal of phosphorus, P-SAD, at Cukα wavelength has been previously demonstrated using Z-DNA. Since the original work on P-SAD with Z-DNA there has been, with a notable exception, a conspicuous absence of applications of the technique to additional nucleic acid crystal structures. We have reproduced the P-SAD phasing of Z-DNA using a rotating-anode source and have attempted to phase a variety of nucleic acid crystals using P-SAD without success. A comparison of P-SAD using Z-DNA and a representative nucleic acid, the Dickerson-Drew dodecamer, is presented along with a S-SAD using only two sulfurs to phase a 2’-thio modified DNA decamer. A theoretical explanation for the limitation of P-SAD applied to nucleic acids is presented to show that the relatively high atomic displacement parameter of phosphorus in the nucleic acid backbone is responsible for the lack of success in applying P-SAD to nucleic acid diffraction data.
Programming Education to Preschoolers: Reflections and Observations from a Field Study

In recent years, there has been a rise in methods and tools dedicated to programming education for chil- dren of primary school age. In this paper, we present our experience of providing five programming ses- sions to a group of eleven children between four and six years. Our sessions followed problem-solving and game-playing themes and featured two newly-developed tools: the unplugged Robot Turtles, and the robotic Ozobot. The activities embed programming concepts such as the order of operations, sym- bolic representations, and functional abstraction. The observations show that children understood and applied concepts such as sorting, sequential operations, and functional abstraction. However, children struggle with giving directions to the object which highlights a spatial awareness limitation. Finally, we link the observations to Piaget’s theory and his limitations to thoughts for children in this age. We find that some of Piaget’s limitations such as egocentrism can explain a few observed behaviors. However, a few limitations contradict our observations such as the irreversibility and transductive reasoning.
living with Obstetric Fistula : Qualitative Research Findings from Bangladesh and the democratic Republic of Congo WhaT Is FIsTUla ?

Obstetric fistula is a condition that most frequently affects women living in resourcepoor countries where, for a variety of reasons, access to emergency obstetric care (EmOC) is difficult. In such settings, women living in rural areas and those from low socioeconomic households have fewer opportunities to obtain EmOC (specifically, a cesarean section) and are therefore more vulnerable to fistula. When not repaired, vaginal fistula causes incontinence, and for some women it can result in an inability to carry and bear children. Because of the physical consequences, fistula stigmatizes women, often forcing them to isolate themselves and remain silent about their condition (Women’s Dignity Project & EngenderHealth, 2006). Due to the nature of the condition, the prevalence of fistula in particular countries is difficult to assess. Few studies have examined what the social consequences are for women with fistula or how the broader social structure in which these women live affects the way they are treated. In this regard, qualitative research was carried out in the countries of Bangladesh and the Democratic Republic of Congo (DRC) to examine the lives of women suffering from fistula, including the physical and social consequences associated with the condition and attempts to obtain care. This brief describes the experiences of these women living in two very different sociocultural contexts.
Predicting Athletes’ Pre-Exercise Fluid Intake: A Theoretical Integration Approach

Pre-exercise fluid intake is an important healthy behavior for maintaining athletes’ sports performances and health. However, athletes’ behavioral adherence to fluid intake and its underlying psychological mechanisms have not been investigated. This prospective study aimed to use a health psychology model that integrates the self-determination theory and the theory of planned behavior for understanding pre-exercise fluid intake among athletes. Participants (n = 179) were athletes from college sport teams who completed surveys at two time points. Baseline (Time 1) assessment comprised psychological variables of the integrated model (i.e., autonomous and controlled motivation, attitude, subjective norm, perceived behavioral control, and intention) and fluid intake (i.e., behavior) was measured prospectively at one month (Time 2). Path analysis showed that the positive association between autonomous motivation and intention was mediated by subjective norm and perceived behavioral control. Controlled motivation positively predicted the subjective norm. Intentions positively predicted pre-exercise fluid intake behavior. Overall, the pattern of results was generally consistent with the integrated model, and it was suggested that athletes’ pre-exercise fluid intake behaviors were associated with the motivational and social cognitive factors of the model. The research findings could be informative for coaches and sport scientists to promote athletes’ pre-exercise fluid intake behaviors.
Sequential Attend, Infer, Repeat: Generative Modelling of Moving Objects

We present Sequential Attend, Infer, Repeat (SQAIR), an interpretable deep generative model for image sequences. It can reliably discover and track objects through the sequence; it can also conditionally generate future frames, thereby simulating expected motion of objects. This is achieved by explicitly encoding object numbers, locations and appearances in the latent variables of the model. SQAIR retains all strengths of its predecessor, Attend, Infer, Repeat (AIR, Eslami et. al. 2016), including unsupervised learning, made possible by inductive biases present in the model structure. We use a moving multi-\textsc{mnist} dataset to show limitations of AIR in detecting overlapping or partially occluded objects, and show how \textsc{sqair} overcomes them by leveraging temporal consistency of objects. Finally, we also apply SQAIR to real-world pedestrian CCTV data, where it learns to reliably detect, track and generate walking pedestrians with no supervision.
Complex Word Identification: Convolutional Neural Network vs. Feature Engineering

We describe the systems of NLP-CIC team that participated in the Complex Word Identification (CWI) 2018 shared task. The shared task aimed to benchmark approaches for identifying complex words in English and other languages from the perspective of non-native speakers. Our goal is to compare two approaches: feature engineering and a deep neural network. Both approaches achieved comparable performance on the English test set. We demonstrated the flexibility of the deep-learning approach by using the same deep neural network setup in the Spanish track. Our systems achieved competitive results: all our systems were within 0.01 of the system with the best macro-F1 score on the test sets except on Wikipedia test set, on which our best system is 0.04 below the best macro-F1 score.
Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.
Seasonal Alterations in Organic Phosphorus Metabolism Drive the Phosphorus Economy of Annual Growth in F. sylvatica Trees on P-Impoverished Soil

Phosphorus (P) is one of the most important macronutrients limiting plant growth and development, particularly in forest ecosystems such as temperate beech (Fagus sylvatica) forests in Central Europe. Efficient tree internal P cycling during annual growth is an important strategy of beech trees to adapt to low soil-P. Organic P (Porg) is thought to play a decisive role in P cycling, but the significance of individual compounds and processes has not been elucidated. To identify processes and metabolites involved in P cycling of beech trees, polar-metabolome and lipidome profiling was performed during annual growth with twig tissues from a sufficient (Conventwald, Con) and a low-soil-P (Tuttlingen, Tut) forest. Autumnal phospholipid degradation in leaves and P export from senescent leaves, accumulation of phospholipids and glucosamine-6-phosphate (GlcN6P) in the bark, storage of N-acetyl-D-glucosamine-6-phosphate (GlcNAc6P) in the wood, and establishing of a phospholipid “start-up capital” in buds constitute main processes involved in P cycling that were enhanced in beech trees on low-P soil of the Tut forest. In spring, mobilization of P from storage pools in the bark contributed to an effective P cycling. Due to the higher phospholipid “start-up capital” in buds of Tut beeches, the P metabolite profile in developing leaves in spring was similar in beech trees of both forests. During summer, leaves of Tut beeches meet their phosphate (Pi) needs by replacing phospholipids by galacto- and sulfolipids. Thus, several processes contribute to adequate Pi supply on P impoverished soil thereby mediating similar growth of beech at low and sufficient soil-P availability.
High-Multiplicity Election Problems 1

The computational study of elections generally assumes that the preferences of the electorate come in as a list of votes. Depending on the context, it may be much more natural to represent the list succinctly, as the distinct votes of the electorate and their counts, i.e., high-multiplicity representation. We consider how this representation affects the complexity of election problems. High-multiplicity representation may be exponentially smaller than standard representation, and so many polynomial-time algorithms for election problems in standard representation become exponentialtime. Surprisingly, for polynomial-time election problems, we are often able to either adapt the same approach or provide new algorithms to show that these problems remain polynomial-time in the high-multiplicity case; this is in sharp contrast to the case where each voter has a weight, where the complexity usually increases. In the process we explore the relationship between high-multiplicity scheduling and manipulation of high-multiplicity elections. And we show that for any fixed set of job lengths, high-multiplicity scheduling on uniform parallel machines is in P, which was previously known for only two job lengths. We did not find any natural case where a polynomial-time election problem does not remain in P when moving to high-multiplicity representation. However, we found one natural NP-hard election problem where the complexity does increase, namely winner determination for Kemeny elections.
Investigation on the Nanomechanics of Liposome Adsorption on Titanium Alloys: Temperature and Loading Effects

The mechanical properties of liposomes, determined by the lipid phase state at ambient temperature, have a close relationship with their physiological activities. Here, atomic force microscopy (AFM) was used to produce images and perform force measurements on titanium alloys at two adsorbed temperatures. The mechanical properties were evaluated under repeated loading and unloading, suggesting a better reversibility and resistance of gel phase liposomes. The liquid phase liposomes were irreversibly damaged during the first approach while the gel phase liposomes could bear more iterations, resulting from water flow reversibly going across the membranes. The statistical data offered strong evidence that the lipid membranes in the gel phase are robust enough to resist the tip penetration, mainly due to their orderly organization and strong hydrophobic interactions between lipid molecules. This work regarding the mechanical properties of liposomes with different phases provides guidance for future clinical applications, such as artificial joints.
Looking Without Landing—Using Remote Piloted Aircraft to Monitor Fur Seal Populations Without Disturbance

Technical advances in monitoring devices, specifically drones, are allowing managers and scientists to obtain quality information on ecosystem health with minimal disturbance to ecosystems and the wildlife they support. Temporal and spatial indicators of ecosystem health, such as population size and/or abundance estimates of marine mammals are the basis for our understanding and prediction of ecosystem change. This is critical for the achievement of conservation goals and sustainable natural resources use. Performing surveys to obtain abundance estimates can be logistically demanding and expensive particularly in offshore marine environments, and can cause significant disturbance to wildlife. These constraints may lead to sub-optimal monitoring programs that reduce the frequency and/or precision of surveys at the cost of data quality and confidence in the resulting analyses. Using Remote Piloted Aircraft (RPAs) can be a solution to this challenge. With appropriate testing and ethical consideration; for many situations, RPAs can perform surveys with increased frequency, higher data resolution and less disturbance than typical methods that involve people being present on the ground, thereby enabling more robust programs for monitoring. We demonstrate the process of testing images from RPAs for estimating the abundance of Australian fur seals (Arctocephalus pusillus doriferus) at one of their largest colonies on Seal Rocks, Australia. Two sizes of quadcopter (1400 mm and 350 mm) with different imaging equipment were tested at 40, 60 and 80 m altitude above sea level. We assessed wildlife disturbance levels and optimised a methodology for effective and economical monitoring of this site. We employed commercially available and open-source software for programming survey flights (Drone Deploy), image processing (Agisoft Photoscan and Autopano Giga), data collation and analyses (R and Python). An online portal was developed to facilitate data collection, with the ultimate goal being the engagement of the public as citizen scientists in fur seal counts from RPA images. Preliminary comparisons show that a small RPA at 40 m altitude can produce pup counts 20-32% higher than corresponding ground counts without observable disturbance. The benefits and disadvantages of the RPA trials are discussed, as well as important considerations for those looking to incorporate similar methodologies in
A High Noise Immunity, 28 × 16-Channel Finger Touch Sensing IC Using OFDM and Frequency Translation Technique

In this paper, a high noise immunity, 28 × 16-channel finger touch sensing IC for an orthogonal frequency division multiplexing (OFDM) touch sensing scheme is presented. In order to increase the signal-to-noise ratio (SNR), the OFDM sensing scheme is proposed. The transmitter (TX) transmits the orthogonal signal to each channels of the panel. The receiver (RX) detects the magnitude of the orthogonal frequency to be transmitted from the TX. Due to the orthogonal characteristics, it is robust to narrowband interference and noise. Therefore, the SNR can be improved. In order to reduce the noise effect of low frequencies, a mixer and high-pass filter are proposed as well. After the noise is filtered, the touch SNR attained is 60 dB, from 20 dB before the noise is filtered. The advantage of the proposed OFDM sensing scheme is its ability to detect channels of the panel simultaneously with the use of multiple carriers. To satisfy the linearity of the signal in the OFDM system, a high-linearity mixer and a rail-to-rail amplifier in the TX driver are designed. The proposed design is implemented in 90 nm CMOS process. The SNR is approximately 60 dB. The area is 13.6 mm2, and the power consumption is 62.4 mW.
Comparison of Four Control Methods for a Five-Choice Assistive Technology

Severe motor impairments can affect the ability to communicate. The ability to see has a decisive influence on the augmentative and alternative communication (AAC) systems available to the user. To better understand the initial impressions users have of AAC systems we asked naïve healthy participants to compare two visual (a visual P300 brain-computer interface (BCI) and an eye-tracker) and two non-visual systems (an auditory and a tactile P300 BCI). Eleven healthy participants performed 20 selections in a five choice task with each system. The visual P300 BCI used face stimuli, the auditory P300 BCI used Japanese Hiragana syllables and the tactile P300 BCI used a stimulator on the small left finger, middle left finger, right thumb, middle right finger and small right finger. The eye-tracker required a dwell time of 3 s on the target for selection. We calculated accuracies and information-transfer rates (ITRs) for each control method using the selection time that yielded the highest ITR and an accuracy above 70% for each system. Accuracies of 88% were achieved with the visual P300 BCI (4.8 s selection time, 20.9 bits/min), of 70% with the auditory BCI (19.9 s, 3.3 bits/min), of 71% with the tactile BCI (18 s, 3.4 bits/min) and of 100% with the eye-tracker (5.1 s, 28.2 bits/min). Performance between eye-tracker and visual BCI correlated strongly, correlation between tactile and auditory BCI performance was lower. Our data showed no advantage for either non-visual system in terms of ITR but a lower correlation of performance which suggests that choosing the system which suits a particular user is of higher importance for non-visual systems than visual systems.
Context-Aware Action Detection in Untrimmed Videos Using Bidirectional LSTM

We consider the problem of action detection in untrimmed videos. We argue that the contextual information in a video is important for this task. Based on this intuition, we design a network using a bidirectional Long Short Term Memory (Bi-LSTM) model that captures the contextual information in videos. Our model includes a modified loss function which enforces the network to learn action progression, and a backpropagation in which gradients are weighted on the basis of their origin on the temporal scale. LSTMs are good at capturing the long temporal dependencies, but not so good at modeling local temporal features. In our model, we use a 3-D Convolutional Neural Network (3-D ConvNet) for capturing the local spatio-temporal features of the videos. We perform a comprehensive analysis on the importance of learning the context of the video. Finally, we evaluate our work on two action detection datasets, namely ActivityNet and THUMOS'14. Our method achieves competitive results compared with the existing approaches on both datasets.