Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycotic corneal ulcers in upper Assam

Purpose: To study the association of various risk factors and epidemiological variables of mycotic keratitis treated at a tertiary referral hospital of upper Assam. Materials and Methods: In this hospital-based prospective study a total of 310 consecutive corneal ulcer cases attending the ophthalmology outpatient department of Assam Medical College were enrolled between April 2007 and March 2009. After clinical and slit-lamp biomicroscopic examination in all suspected cases, smears and culture examination for fungus was done to establish the etiology. Demographic information and associated probable risk factors of individual cases were noted in a predesigned questionnaire. Results: In 188 (60.6%) cases fungal etiology could be established. Out of them 67.6% were males. The most commonly affected age group was 41-50 years (25.5%). The maximum (23.4%) cases were reported during the paddy harvesting season in Assam (January and February). Fungal element could be demonstrated in 65.2% cases in direct potassium hydroxide (KOH) mount. The commonest predisposing factor was corneal injury (74.5%). While diabetes was a significant systemic predisposing factor in mixed bacterial and fungal infections in 11.1% cases, blocked naso-lacrimal duct was the local predisposing factor in 11.1% of cases. Fusarium solani (25%) was the commonest isolate followed by Aspergillus species (19%), Curvularia species (18.5%) and Penicillium species (15.2%). Yeasts were isolated in 2.7% (n=5) cases. Conclusions: Ocular trauma was the commonest cause of fungal corneal ulcer in Assam and Fusarium solani was the commonest species responsible for it. Most of the mycotic ulcer cases come from rural areas including the tea gardens.
Randomized reverse marker strategy design for prospective biomarker validation

We describe a novel study design for validating marker‐based treatment strategies meant to select among possible therapeutic options using a biologic marker. Studying existing designs in realistic scenarios, we demonstrate that this design is more than four times more efficient for testing the interaction between a marker and its intended treatment. Our analysis employs a simple parametric framework that uncovers systematic biases in currently proposed designs and suggests how they may be accommodated or enumerated. In the context of markers for choosing a treatment for recurrent ovarian cancer, our proposal requires sample sizes on the order of recently completed phases II and III studies making validation studies for this clinical decision scenario viable. © 2014 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.
Meal consumption is ineffective at maintaining or correcting water balance in a desert lizard, Heloderma suspectum

SUMMARY Many xeric organisms maintain water balance by relying on dietary and metabolic water rather than free water, even when free water may be available. For such organisms, hydric state may influence foraging decisions, since meal consumption is meeting both energy and water demands. To understand foraging decisions it is vital to understand the role of dietary water in maintaining water balance. We investigated whether meal consumption was sufficient to maintain water balance in captive Gila monsters (Heloderma suspectum) at varying levels of dehydration. Gila monsters could not maintain water balance over long time scales through meal consumption alone. Animals fed a single meal took no longer to dehydrate than controls when both groups were deprived of free water. Additionally, meal consumption imparts an acute short-term hydric cost regardless of hydration state. Meal consumption typically resulted in a significant elevation in osmolality at 6 h post-feeding, and plasma osmolality never fell below pre-feeding levels despite high water content (~70%) of meals. These results failed to support our hypothesis that dietary water is valuable to Gila monsters during seasonal drought. When considered in conjunction with previous research, these results demonstrate that Gila monsters, unlike many xeric species, are heavily reliant on seasonal rainfall and the resulting free-standing water to maintain water balance.
Investigation of the Electrical Characteristics on Measurement Frequency of a Thin-Film Ceramic Humidity Sensor

Efforts have been made by the researchers to enhance the sensitivity of a humidity sensor by selecting and fabricating different nanostructures thin films and optimizing their pore morphology. However, other characteristics, such as nonlinearity, hysteresis, reproducibility, response and recovery times, and selectivity, are equally important for real time measurement, monitoring, and controlling of humidity. It is reported that a low signal frequency is essential for enhanced sensitivity, but the effect of the signal frequency on other characteristics is rarely investigated. We have investigated the role of the signal frequency on the response characteristics of a nanostructure ceramic thin-film interdigitated electrode humidity sensor for the first time. Our studies show that although the sensitivity is high at low frequency, the performance of the sensor is highly nonlinear and frequency dependent. At high frequency above 100 kHz, the sensitivity is reduced, but other characteristics of the sensors are improved significantly. Improved characteristics are due to the reduced effect of double layer capacitance that plays a significant role for extreme sensitivity at low frequency. The effect of double layer capacitance is rarely considered for evaluating the response characteristics in the literatures. Results show that at 200-kHz frequency, nonlinearity and hysteresis are 9.39% and 16.77%, while at 100 Hz, these values are 5588% and 70.8%, respectively. Improve response characteristics will reduce the complexity of signal conditioning, particularly nonlinearity and hysteresis, the compensation of which is essential for almost all types of humidity sensors.
HIV/AIDS awareness among Iraqi medical and dental students

Objectives: The present study investigated the awareness of HIV/AIDS among medical and dental students in four provinces of Iraq, a country with low HIV/AIDS frequency. Materials and Methods: In the present study, the target population was all Iraqi medical and dental students who were in 3rd and 4th year of their education. Out of 15 medicine and 10 dentistry faculties in Iraq, 4 medical and dental faculties were randomly selected. All the students under them were invited to participate in the study (600 students) and 526 responses were received from them. We distributed the questionnaires to students during their obligatory lectures in the academic year 2012–2013. Data collection was done with a self-administered questionnaire containing knowledge and attitude questions (11 questions for each part) in addition to some demographic questions. Results: A total of 526 questionnaires were received (from 319 medical students and 207 dental students). Knowledge of about half of the medical students (54%) was at an intermediate level and of 27.1% students was at a good level; more than half of the dental students (68.2%) had an intermediate level and 10.5% had a good level of knowledge. The level of attitude of medical students was 14.7% at an intermediate level and of dentistry students was 21.4% at an intermediate level. Attitude of none of the students was at good level. Knowledge and attitude scores were not significantly associated with age, gender, or marital status. However, medical students had better knowledge and attitude toward HIV/AIDS, compared to dental students. Conclusions: Some coefficients exist in knowledge and attitude of Iraqi medical and dental students toward HIV/AIDS. Results indicate that more emphasis should be placed on educating dental and medical students about HIV and other blood-borne infections.
Multi-Scale Convolutional Neural Networks for Time Series Classification

Time series classification (TSC), the problem of predicting class labels of time series, has been around for decades within the community of data mining and machine learning, and found many important applications such as biomedical engineering and clinical prediction. However, it still remains challenging and falls short of classification accuracy and efficiency. Traditional approaches typically involve extracting discriminative features from the original time series using dynamic time warping (DTW) or shapelet transformation, based on which an off-the-shelf classifier can be applied. These methods are ad-hoc and separate the feature extraction part with the classification part, which limits their accuracy performance. Plus, most existing methods fail to take into account the fact that time series often have features at different time scales. To address these problems, we propose a novel end-to-end neural network model, Multi-Scale Convolutional Neural Networks (MCNN), which incorporates feature extraction and classification in a single framework. Leveraging a novel multi-branch layer and learnable convolutional layers, MCNN automatically extracts features at different scales and frequencies, leading to superior feature representation. MCNN is also computationally efficient, as it naturally leverages GPU computing. We conduct comprehensive empirical evaluation with various existing methods on a large number of benchmark datasets, and show that MCNN advances the state-of-the-art by achieving superior accuracy performance than other leading methods.
Scalable stability conditions for heterogeneous networks via integral quadratic constraints

Decentralised and scalable conditions for robust stability of networks of heterogenous linear time-invariant (LTI) systems are derived based on integral quadratic constraints. These generalise previous works in the literature with an increased flexibility in the choice of multipliers employed. The results allow for arbitrary interconnection matrices and accommodate multi-input-multi-output systems. Similar conditions are also developed for nonlinear systems interconnected with LTI systems following a bipartite structure. In particular, the stability certificates only involve each individual LTI agent and its nearest nonlinear neighbours.
Combinatorial Networks Regulating Seed Development and Seed Filling

Seeds offer plants a unique opportunity to suspend their life cycles in a desiccated state. This enables them to endure adverse environmental conditions and then resume growth by using endogenous storage products when more favorable conditions develop. Seed development is pivotal to the reproductive success of flowering plants (Angiosperms). It is initiated by the process of double fertilization that gives rise to the embryo and the endosperm. The embryo develops following fertilization of the haploid egg cell by one of the sperm cells leading to the formation of a diploid zygote. In contrast, the triploid endosperm results from the fertilization of the maternal homodiploid central cell of the ovule by another sperm cell (Weterings & Russell, 2004). The diploid embryo and the triploid endosperm develop concertedly inside the maternal ovule and are protected by a seed coat constituted of maternally derived inner and outer integuments. The seed coat provides an important interface between the embryo and the external environment (Haughn & Chaudhury, 2005). Thus, different genome combinations contribute to seed ontogeny.
Genotype-Dependent Interaction of Lentil Lines with Ascochyta lentis

Ascochyta blight of lentil is a prevalent disease in many lentil producing regions and can cause major yield and grain quality losses. The most environmentally acceptable and economically profitable method of control is to develop varieties with high levels of durable resistance. Genetic studies to date suggest that ascochyta blight resistance genes (R-gene) in lentil lines CDC Robin, ILL 7537, 964a-46, and ILL 1704 are non-allelic. To understand how different R-genes manifest resistance in these genotypes and an accession of Lens ervoides, L-01-827A, with high level of resistance to ascochyta blight, cellular and molecular defense responses were compared after inoculation with the causal pathogen Ascochyta lentis. Pathogenicity testing of the resistant lines to A. lentis inoculation revealed significantly lower disease severity on CDC Robin and ILL 7537 compared to ILL 1704 and 964a-46, and no symptoms of disease were observed on L-01-827A. Histological examinations indicated that cell death triggered by the pathogen might be disrupted as a mechanism of resistance in CDC Robin. In contrast, limiting colonization of epidermal cells by A. lentis is a suggested mechanism of resistance in 964a-46. A time-series comparison of the expressions of hallmark genes in salicylic acid (SA) and jasmonic acid (JA) signal transduction pathways between CDC Robin and 964a-46 was conducted. These partially resistant genotypes differed in the timing and the magnitude of SA and JA signaling pathway activation. The SA signaling pathway was only triggered in 964a-46, whereas the JA pathway was triggered in both partially resistant genotypes CDC Robin and 964a-46. The expression of JA-associated genes was lower in 964a-46 than CDC Robin. These observations corroborate the existence of diverse ascochyta blight resistance mechanisms in lentil genotypes carrying different R-genes.
Microbial reduction efficacy of various disinfection treatments on fresh-cut cabbage

To reduce the pathogenic microorganisms of fresh-cut vegetables, various sanitizers applied at different concentrations and against four different bacteria inoculated in high or low initial loads were tested on shredded cabbage. The bacteria were reduced by 1 log CFU g−1 after being exposed to over 100 ppm sodium hypochlorite, over 1% hydrogen peroxide, over 50 ppm peroxyacetic acid, and three types of electrolyzed water (EW) for 1 min. When the efficacy of the sanitizer was compared in the low initial bacterial load of 103–104 CFU g−1, a significant reduction in the inoculated bacteria was observed with the acidified EW treatment, followed by the 50 ppm peroxyacetic acid and the neutral EW treatment, which was more efficient than the 100 ppm sodium hypochlorite treatment. The efficacy of the various sanitizers used could be also influenced by different bacterial species.
Potent Nonnucleoside Reverse Transcriptase Inhibitors Target HIV-1 Gag-Pol

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) target HIV-1 reverse transcriptase (RT) by binding to a pocket in RT that is close to, but distinct, from the DNA polymerase active site and prevent the synthesis of viral cDNA. NNRTIs, in particular, those that are potent inhibitors of RT polymerase activity, can also act as chemical enhancers of the enzyme's inter-subunit interactions. However, the consequences of this chemical enhancement effect on HIV-1 replication are not understood. Here, we show that the potent NNRTIs efavirenz, TMC120, and TMC125, but not nevirapine or delavirdine, inhibit the late stages of HIV-1 replication. These potent NNRTIs enhanced the intracellular processing of Gag and Gag-Pol polyproteins, and this was associated with a decrease in viral particle production from HIV-1-transfected cells. The increased polyprotein processing is consistent with premature activation of the HIV-1 protease by NNRTI-enhanced Gag-Pol multimerization through the embedded RT sequence. These findings support the view that Gag-Pol multimerization is an important step in viral assembly and demonstrate that regulation of Gag-Pol/Gag-Pol interactions is a novel target for small molecule inhibitors of HIV-1 production. Furthermore, these drugs can serve as useful probes to further understand processes involved in HIV-1 particle assembly and maturation.
Efficient Anomaly Detection by Isolation Using Nearest Neighbour Ensemble

This paper presents iNNE (isolation using Nearest Neighbour Ensemble), an efficient nearest neighbour-based anomaly detection method by isolation. Inne runs significantly faster than existing nearest neighbour-based methods such as Local Outlier Factor, especially in data sets having thousands of dimensions or millions of instances. This is because the proposed method has linear time complexity and constant space complexity. Compared with the existing tree-based isolation method iForest, the proposed isolation method overcomes three weaknesses of iForest that we have identified, i.e., Its inability to detect local anomalies, anomalies with a low number of relevant attributes, and anomalies that are surrounded by normal instances.
Variations in cyclic fatigue resistance among ProTaper Gold, ProTaper Next and ProTaper Universal instruments at different levels.

AIM To compare the cyclic fatigue resistance of ProTaper Gold (PTG, Dentsply Tulsa Dental Specialities, Tulsa, OK, USA), ProTaper Next (PTN, Dentsply Tulsa Dental Specialities) and ProTaper Universal (PTU, Dentsply Tulsa Dental Specialities) instruments at different levels. METHODOLOGY A total of 72 files were used to evaluate the cyclic fatigue of PTU (F2), PTN (X2) and PTG (F2) at 5 mm (n = 12) and 8 mm (n = 12) from the tip in 3-mm-radius steel canals with a 60° angle of curvature. The time to fracture was recorded. The Kolmogorov-Smirnov test was used to assess the normality of the samples distribution, and the statistical analysis was performed using the independent sample t-test (P < 0.01). RESULTS Significant differences were found amongst the instruments 5 mm from the tip (P < 0.01). The PTG files had the highest CF resistance, and the PTN files displayed greater CF resistance than the PTU files. No significant differences were found between the PTG and PTN files 8 mm from the tip (P > 0.01). The PTG and PTN files demonstrated greater CF resistance than the PTU files (P < 0.01). CONCLUSIONS The PTG instruments were the most resistant 5 and 8 mm from the tip; however, at 8 mm, there was no difference between the PTG and PTN instruments. The PTU files had the lowest CF resistance at all levels.
Lessons from Interval Gastric Cancer: Read between the Lines

The term “interval gastric cancer (IGC)” is probably used only in Far East countries such as Korea and Japan where nationwide screening programs for gastric cancer has been established. For Western doctors, interval colorectal cancer may be a more familiar corresponding term.1 Quality of colonoscopy has been reported to be the most important factor for the development of interval colorectal cancer.2 In this Korean study, the authors reported location of the lesion and tumor differentiation as two predictors of IGC.3 IGC was more common in tumors located at the lower body of the stomach and in tumors with undifferentiated carcinoma. Previous reports revealed that IGC was more common in upper gastrointestinal series screening groups compared to endoscopy groups.4 To sum these results, meticulous examination during endoscopy seems to be mandatory to reduce IGC. However, additional studies are anticipated to clarify the reasons why tumor location and differentiation affected the development of IGC. Although there has been no definite evidence, it is plausible that undifferentiated carcinoma grows rapidly compared to differentiated carcinoma, which resulted in increased proportion of IGC. As for the location, the authors did not describe how many pictures per person were analyzed and couldn’t analyze whether blind spots were more common in the lower body of stomach. IGC includes both missed lesions and latent lesions. Missed lesions can be decreased with meticulous examination such as chromoendoscopy and/or new image-enhanced endoscopy with biopsy, while development of latent lesions may be inevitable. Pretreatment before endoscopy with proteolytic enzymes is another option to improve the visibility of endoscopy.5 Quality control is also an issue. Experience of endoscopists might influence the development of IGCs and endoscopists should be vigilant to avoid blind spots. Currently, the Korean Society of Gastrointestinal Endoscopy recommends eight cuts as standard pictures for esophagogastroduodenoscopy (EGD) which includes only four images of the stomach. This was initially suggested by the European guidelines.6 However, gastric cancer is more common in Korea than in Europe and new guidelines for standard picturization during EGD should be established in the near future. We also should reconsider whether the Korean national cancer screening program consisting of biennial endoscopy is optimal in Korea. When screening was performed within 2 years, half of the lesions might be treated by endoscopic resection.7 However, debates on the interval of screening endoscopy still exists, especially in patients with severe intestinal metaplasia (IM). 8 The authors of this article described that background atrophy and IM of the stomach were related to development of IGC. It is plausible that unevenness of gastric mucosa in IM prevents the endoscopists’ from detecting minimal and/or minute gastric cancer.9 In conclusion, meticulous examination by endoscopy might reduce the development of IGC in Korea. Educational programs to improve the quality of endoscopists should be continued and improved.
Stability of genetic regulatory networks with time delay

Presents a model for genetic regulatory networks with time delays, which is described by functional differential equations or delay differential equations (DDE), provide necessary and sufficient conditions for simplifying the genetic network model, and further analyze nonlinear properties of the model in terms of local stability and bifurcation. The proposed model transforms the original interacting network into several simple transcendental equations at an equilibrium, thereby significantly reducing the computational complexity and making analysis of stability and bifurcation tractable for even large-scale networks. Finally, to test the theory, a repressilator model is used as an example for numerical simulation.
Training LDCRF model on unsegmented sequences using connectionist temporal classification

Many machine learning problems such as speech recognition, gesture recognition, and handwriting recognition are concerned with simultaneous segmentation and labeling of sequence data. Latent-dynamic conditional random field (LDCRF) is a well-known discriminative method that has been successfully used for this task. However, LDCRF can only be trained with pre-segmented data sequences in which the label of each frame is available apriori. In the realm of neural networks, the invention of connectionist temporal classification (CTC) made it possible to train recurrent neural networks on unsegmented sequences with great success. In this paper, we use CTC to train an LDCRF model on unsegmented sequences. Experimental results on two gesture recognition tasks show that the proposed method outperforms LDCRFs, hidden Markov models, and conditional random fields.
Effect of natural pozzolana and polypropylene fibers on the performance of lime mortar for old buildings restoration

Abstract The main objective of this research is to elaborate a mortar based on lime (L), pozzolana (PZ) and polypropylene fibers (PP) to restore and renovate the stone constructions while maintaining their initial comfort. Unlike the new buildings, in rehabilitation, we have to deal with the existing ones. For this purpose, mortars samples from an old building, chosen as cases of study, were taken and chemically analyzed in order to reproduce their equivalent mortars. Three different mortars were made and studied. A lime based mortar (M1), lime-pozzolana based mortar (M2) and lime-pozzolana based mortar with polypropylene fibers (M3). In order to preserve the thermal comfort offered by the old building, the thermal conductivity and the mechanical proprieties were studied. The adhesion of each mortar was also tested on several support types (concrete, concrete block, brick and natural stone). Finally, the three studied mortars were applied on the facade of the chosen building. The results are satisfactory on both levels aesthetic and adhesion. The incorporation of polypropylene fibers was more promising regarding thermal comfort. Moreover, their use lightened the matrix and improved the tensile strength.