Miracle-dz/UniFAR-FTUs huggingface dataset:
Biological applications, visualizations, and extensions of the long short-term memory network

Sequences are ubiquitous in the domain of biology. One of the current best machine learning techniques for analysing sequences is the long short-term memory (LSTM) network. Owing to significant barriers to adoption in biology, focussed efforts are required to realize the use of LSTMs in practice. Thus, the aim of this work is to improve the state of LSTMs for biology, and we focus on biological tasks pertaining to physiological signals, peripheral neural signals, and molecules. This goal drives the three subplots in this thesis: biological applications, visualizations, and extensions. We start by demonstrating the utility of LSTMs for biological applications. On two new physiological-signal datasets, LSTMs were found to outperform hidden Markov models. LSTM-based models, implemented by other researchers, also constituted the majority of the best performing approaches on publicly available medical datasets. However, even if these models achieve the best performance on such datasets, their adoption will be limited if they fail to indicate when they are likely mistaken. Thus, we demonstrate on medical data that it is straightforward to use LSTMs in a Bayesian framework via dropout, providing model predictions with corresponding uncertainty estimates. Another dataset used to show the utility of LSTMs is a novel collection of peripheral neural signals. Manual labelling of this dataset is prohibitively expensive, and as a remedy, we propose a sequence-to-sequence model regularized by Wasserstein adversarial networks. The results indicate that the proposed model is able to infer which actions a subject performed based on its peripheral neural signals with reasonable accuracy. As these LSTMs achieve state-of-the-art performance on many biological datasets, one of the main concerns for their practical adoption is their interpretability. We explore various visualization techniques for LSTMs applied to continuous-valued medical time series and find that learning a mask to optimally delete information in the input provides useful interpretations. Furthermore, we find that the input features looked for by the LSTM align well with medical theory. For many applications, extensions of the LSTM can provide enhanced suitability. One such application is drug discovery – another important aspect of biology. Deep learning can aid drug discovery by means of generative models, but they often produce invalid molecules
Learning to Minify Photometric Stereo

Photometric stereo estimates the surface normal given a set of images acquired under different illumination conditions. To deal with diverse factors involved in the image formation process, recent photometric stereo methods demand a large number of images as input. We propose a method that can dramatically decrease the demands on the number of images by learning the most informative ones under different illumination conditions. To this end, we use a deep learning framework to automatically learn the critical illumination conditions required at input. Furthermore, we present an occlusion layer that can synthesize cast shadows, which effectively improves the estimation accuracy. We assess our method on challenging real-world conditions, where we outperform techniques elsewhere in the literature with a significantly reduced number of light conditions.
Research Article Genetic and biochemical biomarkers related to oxidative stress in patients with schizophrenia

We evaluated the association of glutathione Stransferase polymorphisms (GSTT1 and GSTM1) and oxidative stress biomarkers in patients with schizophrenia. A total of 162 subjects were studied: 53 had schizophrenia (Total Study Group-TSG), and 109 without the disorder (Total Control Group-TCG). To analyze oxidative stress, TSG was distributed into treatment-responsive schizophrenia (N = 26) and treatment-resistant (N = 27) versus
The Effect of the Extent of the Exposure and Concentration for the Three Types of Surface Treatment in the Mortality of Larvae and Adults of Confused Flour Beetle, Tribolum confusum (Du Val)

Two concentrations (0.1, 0.05 Mg/L) of chemical insecticides Lambda cyhalothrine were used in combination with Castor oil (Ricinus communis) in mixtures of 1:1, 1:2 and 1:3 ratio of insecticide: castor oil for their effect to the mortality of larvae and adult of confused flour beetle, Tribolium confusum (Du Val) which exposed to different surface substrates (aluminum, cardboard, and wood surfaces). The mortality data were recorded after 24 and 48 hours. The calculated mortality in aluminum surfaces were 53.00%, 56.00% and 62.00% in 1:1, 1:2 and 1:3 mixing ratio, respectively, after 24 hours, in adults. With the cardboard treatment, the mortality were 43.00%, 56.00% and 57.66% in 1:1, 1:2 and 1:3 mixing ratio, respectively, in the same treatment time. Whereas in wood surface the mortality were 56.33%, 58.00% and 61.00% in 1:1, 1:2 and 1:3 mixing ratio, respectively, in the same treatment time. The results showed that 1:3 mixing ratio had the higher mortality ratio and the 1:1 mixing ratio had the least mortality against T. confusum. The results also revealed that all tested mix ratios are more efficacies on aluminum surface followed by cardboard and wood surface, respectively. In general, efficacy was the best on non-porous surfaces compared with more porous surfaces.
DO CHRONIC DISEASE SELF-MANAGEMENT PROGRAMS FOR INDIVIDUALS LIVING WITH HIV/AIDS PROMOTE SELF-EFFICACY AND DO THEY IMPROVE HEALTH OUTCOMES?

iii ACKNOWLEDGEMENTS . v LIST OF TABLES . x LIST OF FIGURES . xi CHAPTER ONE: INTRODUCTION Introduction . 1 Problem Statement . 8 Purpose of Study . 9 Significance of the Project for Social Work Practice . 14 CHAPTER TWO: LITERATURE REVIEW Introduction . 17 Self-Management Skills and the Promotion of Self-Efficacy . 18 Chronic Disease Self-Management Programs (CDSPs) for individuals living with HIV/AIDS . 23 Self-Help Mutual Aid Model . 25 Peer Educators . 27 Theories Guiding Conceptualization . 30 Summary . 34 CHAPTER THREE: METHODS Introduction . 36 Study Design . 37 Sampling . 38 Data Collection and Instruments . 40
Genetic programming based predictions and estimations for the endurance and retention of NAND flash memory devices

Genetic Programming Based Predictions and Estimations for the Endurance and Retention of NAND Flash Memory Devices by Damien Hogan The central hypothesis of this thesis is that it is possible to use a supervised machine learning technique, Genetic Programming (GP), to make accurate predictions and estimations regarding the endurance and retention of multi-level cell NAND Flash Memory devices. The retention of storage locations, or blocks, within these devices is the length of time for which they successfully retain their data, while their endurance is the number of times they can be programmed and erased prior to failure. Manufacturers currently place conservative specifications on their devices since there is no technique available to quickly determine the actual endurance and retention capabilities of blocks within them. An extensive empirical evaluation of a number of MLC NAND Flash devices is completed, identifying features for use with GP, before expressions are evolved to make predictions and estimations regarding the retention and endurance of blocks. The empirical evaluation highlights the large variations in performance between blocks in different devices of the same specification, and even between blocks within the same device. As well as building a data set for later use with GP, the durations of program and erase operations are identified as features with which to make endurance predictions and estimations, while a relationship between block location and endurance is also established. GP is employed to evolve binary classification expressions, referred to as retention period classifiers, to predict whether blocks will correctly retain their data for a specified length of time. Following this, endurance classifiers are evolved to predict whether blocks will successfully complete a predefined number of cycles. Finally, symbolic regression expressions are evolved, building on the earlier experiments, to estimate the actual number of cycles each block will complete prior to failure and are referred to as endurance estimators.
Characterizing wing tears in common pipistrelles (Pipistrellus pipistrellus): investigating tear distribution, wing strength, and possible causes

Bats have large, thin wings that are particularly susceptible to tearing. Anatomical specializations, such as fiber reinforcement, strengthen the wing and increase its resistance to puncture, and an extensive vasculature system across the wing also promotes healing. We investigated whether tear positioning is associated with anatomy in common pipistrelles (Pipistrellus pipistrellus). Wing anatomy was described using histological techniques, imaging, and material testing. Tear information, including type, position, time in rehabilitation, and possible causes, was collected from rehabilitators of injured bats across the United Kingdom. Results suggest that the position of the plagiopatagium (the most proximal wing section to the body), rather than its anatomy, influenced the number, location, and orientation of wing tears. While material testing did not identify the plagiopatagium as being significantly weaker than the chiropatagium (the more distal sections of the wing), the plagiopatagium tended to have the most tears. The position of the tears, close to the body and toward the trailing edge, suggests that they are caused by predator attacks, such as from a cat (Felis catus), rather than collisions. Consistent with this, 38% of P. pipistrellus individuals had confirmed wing tears caused by cats, with an additional 38% identified by rehabilitators as due to suspected cat attacks. The plagiopatagium had the lowest number of blood vessels and highest amounts of elastin fibers, suggesting that healing may take longer in this section. Further investigations into the causes of tears, and their effect on flight capabilities, will help to improve bat rehabilitation.
Possible Roles of BELL1 and Class III Homeodomain-Leucine Zipper Genes during Integument Evolution

Premise of research. According to the neosynangial hypothesis, sterilization of megasporangia and compaction of fertile appendages bearing megasporangia were critical steps for integument evolution. Ovules of bell1 (bel1) mutants in Arabidopsis thaliana can form ectopic nucelli in the chalazal domain instead of inner and outer integuments, while distances between ectopic nucelli expand when class III homeodomain-leucine zipper (HD-ZIPIII) genes are compromised in addition to bel1. These phenotypes imply that BEL1 and HD-ZIPIII genes would be participants in the sterilization and compaction steps, respectively. However, this interpretation is challenged by the observation that bel1 ovules also form an outgrowth in the chalazal domain. The outgrowth finally develops into a carpel-like structure (i.e., the ectopic nucelli would be formed on the placenta of this ectopic carpel). We revisited bel1 phenotypes to rule out this possibility and inferred how these genes contributed to integument evolution. Methodology. We observed development and expression of a carpel identity marker CRABS CLAW (CRC) in bel1 ovules. We compared expression of SPOROCYTELESS/NOZZLE (SPL/NZZ), a master regulator of nucellus formation, between bel1 and wild-type carpels by quantitative real-time polymerase chain reaction. We observed accumulation of PIN-FORMED 1 (PIN1) protein in triple mutants of HD-ZIPIII genes. Pivotal results. Morphological observation, as well as expression of CRC, suggested that ectopic nucelli are formed before induction of carpel identity. BEL1 represses SPL/NZZ expression. PIN1 expression was not altered in triple mutants of HD-ZIPIII genes, suggesting that they do not repress the nucellus-promoting pathway(s). Conclusions. The bel1 phenotype suggests that seed plant ovules have a repressed ability to form multiple nucelli, similar to fertile appendages of progymnosperms. BEL1 would have promoted sterilization of megasporangia by repressing SPL/NZZ. HD-ZIPIII genes would have controlled spacing between megasporangia in fertile appendages by regulating the size of the meristematic area rather than by repressing formation of extra megasporangia.
Elevated levels of betatrophin in patients with newly diagnosed diabetes

Introduction. Betatrophin is primarily produced in the liver and regulates the metabolism of triglycerides. Its elevated concentration might be associated with an increased risk of type 2 diabetes. The aim of the study was to evaluate the impact of betatrophin on beta cell function and to compare the concentration of betatrophin in patients newly diagnosed with type 1 diabetes mellitus (T1DM including LADA), type 2 diabetes mellitus (T2DM) and a control group (CG) of healthy volunteers. Patients and methods. The study included 210 patients with newly diagnosed diabetes (70 with T1DM, 140 with T2DM) and 70 CG. To evaluate the relationship between betatrophin and insulin secretion, a glucagon stimulation test was conducted. Results. Serum betatrophin concentrations were signi­ficantly elevated in T1DM and T2DM in comparison to the control group (3.47 [Q1 = 2.28, Q3 = 4.54] in T1DM vs. 1.81 [Q1 = 1.04, Q3 = 2.67] ng/ml in CG, p < 0.001; 3.12 [Q1 = 1.89, Q3 = 4.48] in T2DM vs. 1.81 [Q1 = 1.04, Q3 = 2.67] ng/ml in CG, p < 0.001). No statistically significant differences in betatrophin concentration were observed between the T1DM and T2DM groups. Significant correlations were established between betatrophin, triglyceride (TG) and high-density lipopro­tein (HDL) levels in all study participants, and C-peptide in the T1DM group. Conclusions. Betatrophin concentration was signi­ficantly elevated in patients with newly diagnosed T1DM and T2DM, compared to the control group and could be a biomarker of diabetes. Our study provided evidence which supports the impact of betatrophin on lipid metabolism. The positive correlation between betatrophin and C-peptide in the T1DM group suggests that betatrophin is associated with insulin secretion in T1DM.
Small Business Crews As High Performance Work Teams: The Role Of Vertical And Horizontal Familiarity

ii Dedication.iii Acknowledgements.iv Chapter 1: Introduction.1 Intended Contribution.4 Fluid Teams Literature Review.7 Team Familiarity Literature Review.12 Team Leadership Literature Review.20 Chapter 2: Formal Model and Hypothesis Development.28 Horizontal Team Familiarity.34 Operational and Financial Team Performance.35 Hierarchical Team Familiarity.37 Vertical Team Familiarity and Team Competence.39 Chapter 3: Design and Methodology.44 Operationalization of Independent Variables.46 Operationalization of Dependent Variable.47 Operationalization of Control Variables.50 Data Analysis.53 Chapter 4: Discussion of Results.58
License Number Plate Recognition using Template Matching and Bounding Box Method

Recognition of vehicle number plates is very important in the field of transportation security systems. Template matching is one of the most popular techniques used for number plate recognition. This algorithm works by evaluating the image pattern that will be recognized and then comparing it with the image pattern in the template. A number plate is an object in an image that has many characters which usually consists of numbers and letters. Character recognition cannot be done simultaneously in an image. A number plate object in the image needs to be done early processing, normalization, and segmentation to recognize the character. While to separate each character, a bounding box algorithm is used. This technique is relatively simple and has fast computing. So this study examines a combination of template matching and bounding box methods to detect Indonesian car license plates. Based on the tests that have been done, the accuracy reaches 80%.
Soil and landscape affecting technology transfer targeting subsistence farmers in central Tanzania

Abstract This article deals with technology transfer from science to agriculture with pearl millet (Pennisetum glaucum (L.)R.Br. ) in central Tanzania as example. The major question is which validity recommendations from different types of field experiments have and how geo-information (i.e. soil and landscape position) can lead to more site-specific recommendations. Tied ridging and reduced amounts of placed fertilizer during sowing were tested to increase yields on researcher-managed plots on-station, demonstration plots in villages, and farmer-managed plots on-farm. While on-station trials provided potential yield effects, physical distance to the station and differing conditions led to a higher informational value of village plots that mirror the context of local farmers. The treatments often resulted in significant yield increase. Soil and relief information and distance to settlements (i.e. gradient of management intensity) are key factors for data variability in on-farm trials. Unexplained variability is introduced through leaving degrees of freedom with respect to management to the farmer. Apart from soil and physiographic information, the latter should be part of a detailed data collection procedure in agronomic trials in large numbers addressing Sub-Saharan smallholder farming. Balanced data sets with dispersed trials on crucial soil and relief units are essential for future research.
Commissural white matter disconnectivity in normal ageing and Alzheimer’s disease

The network of commissural white matter fibres responsible for connecting the hemispheres of the brain is known as the corpus callosum (CC). Atrophy to the CC is evident in studies of aging and Alzheimer’s disease (AD), but patterns and functional implications of neurodegeneration are still somewhat unclear. In this thesis, neuroimaging methods were used to further examine how structural and functional CC properties are affected by normal ageing and AD. In Study 1, diffusion tensor imaging (DTI) was used to examine the posterior CC tract bundles in young and older adults. Parietal and temporal midsagittal CC segments were particularly impaired in older adults, while occipital tracts were relatively preserved. Study 2 applied this methodology to study Mild Cognitive Impairment (MCI) and AD. MCI patients exhibited reduced integrity in midsagittal parietal segments compared to controls. AD patients exhibited reductions in parietal and temporal segments, yielding high classification accuracy (95-98%) against controls. Study 3 assessed visual interhemispheric transfer in aging using electroencephalography (EEG). Transfer speed was elongated in older adults, but was driven by earlier activation of the input hemisphere rather than delayed activation of the receiving hemisphere. This was not interpreted as impairment in older age, in line with findings of preserved occipital tracts in Study 1. Study 5 examined EEG functional connectivity methodology. We showed that connectivity was strongest at the dominant EEG frequency, which experiences slowing in older age. Previous studies using conventional frequency bands may therefore be biased against older adults. Study 6 applied these findings to study interhemispheric functional connectivity in older adults, while controlling for age-related frequency slowing. Age-related disconnectivity between frontal sites was evident, reflecting typical anterior-posterior neurodegeneration in older adults (Bennett, Madden, Vaidya, Howard, & Howard, 2010). These studies provide novel spatial and methodological insight into the CC during ageing and AD.
Brain Tumor Detection Using Modified Histogram Thresholding-Quadrant Approach

In medical image processing brain tumor detection is one of the challenging task, since brain images are complicated and tumors can be analyzed only by expert physicians. So In this paper brain tumor is detected at various levels. First the pre-processing is done by median filter in order to reduce noise and then edge detection is done by using canny filter, then Segmentation is done by means of histogram clustering in which the tumor affected image is divided into quadrants and threshold value is set , based on this value tumor is detected. Secondly the other technique involved is superimposing of the tumor affected with the healthy image. This method does not require any initialization while the others require an initialization inside the tumor. The third method in which, the histogram is calculated and the threshold is fixed. This work is carried in MRI image. The experimental results illustrate the usefulness of the new method.
Symbol Digit Modalities Test(SDMT)의 유용성

알쯔하이머형 치매와 피질하 혈관성 치매를 치매초기에 변별하기는 쉽지 않다. 본 연구는 Symbol Digit Modalities Test가 이 두 환자 집단을 잘 변별해낼 수 있는지 확인하고자 수행 되었다.
Combined Real-Time Three-Dimensional Hysterosalpingo-Contrast Sonography with B Mode Hysterosalpingo-Contrast Sonography in the Evaluation of Fallopian Tube Patency in Patients Undergoing Infertility Investigations

Objective This prospective study aimed to investigate the use of real-time three-dimensional hysterosalpingo-contrast sonography (4D-HyCoSy), using contrast agent SonoVue, with B mode hysterosalpingo-contrast sonography (B mode-HyCoSy), to evaluate tubal patency and the wall of the Fallopian tubes in infertility patients. Method In total, we recruited 739 women with fertility requirements from the First Affiliated Hospital of Shantou Medical College between January 2017 and July 2018. All cases received 4D-HyCoSy using contrast agent SonoVue, immediately followed by the B mode-HyCoSy. Of these patients, 145 showed pathological findings in the Fallopian tubes during HyCoSy; 34 of these (62 Fallopian tubes) were verified by laparoscopy and the dye test against routine reference standards. Sonographic findings, along with laparoscopic findings and dye test results, were used to compare the two techniques using the Cohen kappa coefficient. We also investigated the duration of examination and pain score. Results Compared with laparoscopy and the dye test, the tubal occlusion diagnostic accordance rates for 4D-HyCoSy were 88.7% (32+23)/62, with a kappa coefficient of 0.769 and a 76.9% agreement rate. Distal occlusion diagnostic accordance rates for 4D-HyCoSy were 100% (8/8) with a k coefficient of 1.000 and a 100% agreement rate. Conclusions The use of 4D-HyCoSy, with B mode-HyCoSy, for the diagnosis of tubal patency is safe, feasible, noninvasive, and highly accurate. B mode-HyCoSy allowed us to observe tubal walls in an intuitive manner.
A Comparison of Picture to Word Training and Word to Word Training on Native English Speaking College Students’ Acquisition of Italian Vocabulary

The current study assessed the effects of two teaching stimulus presentations, i.e. picture to word and word to word, used to teach second language vocabulary to college students. It also evaluated the emergence of untaught relations when picture to word and word to word were used separately as a teaching strategy. The findings showed picture to word training resulted in more untaught relations. Several aspects such time allotted for online quizzes, experimental and teaching arrangements and vocabulary complexity were suggested for future research.