Miracle-dz/UniFAR-FTUs huggingface dataset:
SRAMM: Short Read Alignment Mapping Metrics

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering process of aligned short reads for various downstream applications. SRAMM is compatible with Python 2.6+ and Python 3.6+ on all operating systems. It works with any short read aligner that generates SAM/BAM/CRAM file outputs and reports 'AS' tags. It is freely available under the MIT license at http://github.com/achon/sramm.
Immunization of Pruning Attack in DNN Watermarking Using Constant Weight Code

To ensure protection of the intellectual property rights of DNN models, watermarking techniques have been investigated to insert side-information into the models without seriously degrading the performance of original task. One of the threats for the DNN watermarking is the pruning attack such that less important neurons in the model are pruned to make it faster and more compact as well as to remove the watermark. In this study, we investigate a channel coding approach to resist the pruning attack. As the channel model is completely different from conventional models like digital images, it has been an open problem what kind of encoding method is suitable for DNN watermarking. A novel encoding approach by using constant weight codes to immunize the effects of pruning attacks is presented. To the best of our knowledge, this is the first study that introduces an encoding technique for DNN watermarking to make it robust against pruning attacks.
Do Small Firms Implement Enterprise Systems Differently? The Case of E-Silk Route Ventures

The cost effectiveness, ease of learning, connectedness and in-depth analytical capabilities provided through cloud computing technologies, have provided small firms the opportunity to implement enterprise systems (ES), which was reserved only for the much resourceful firms. However, it is evident that small firms are still struggling to attain purported benefits of ES and still find it difficult to manage complexities of ES implementations. Further, limited research has been conducted that discusses ES implementation in small firms. This research is an attempt to further the understanding of ES-implementation of small firms and re-evaluate the applicability of fundamental critical success factors to small firms.
HIDA: Towards Holistic Indoor Understanding for the Visually Impaired via Semantic Instance Segmentation with a Wearable Solid-State LiDAR Sensor

Independently exploring unknown spaces or finding objects in an indoor environment is a daily but challenging task for visually impaired people. However, common 2D assistive systems lack depth relationships between various objects, resulting in difficulty to obtain accurate spatial layout and relative positions of objects. To tackle these issues, we propose HIDA, a lightweight assistive system based on 3D point cloud instance segmentation with a solid-state LiDAR sensor, for holistic indoor detection and avoidance. Our entire system consists of three hardware components, two interactive functions (obstacle avoidance and object finding) and a voice user interface. Based on voice guidance, the point cloud from the most recent state of the changing indoor environment is captured through an on-site scanning performed by the user. In addition, we design a point cloud segmentation model with dual lightweight decoders for semantic and offset predictions, which satisfies the efficiency of the whole system. After the 3D instance segmentation, we post-process the segmented point cloud by removing outliers and projecting all points onto a top-view 2D map representation. The system integrates the information above and interacts with users intuitively by acoustic feedback. The proposed 3D instance segmentation model has achieved state-of-the-art performance on ScanNet v2 dataset. Comprehensive field tests with various tasks in a user study verify the usability and effectiveness of our system for assisting visually impaired people in holistic indoor understanding, obstacle avoidance and object search.
Multi-Node Vehicular Wireless Channels: Measurements, Large Vehicle Modeling, and Hardware-in-the-Loop Evaluation

Understanding multi-node vehicular wireless communication channels is crucial for future time-sensitive safety applications for human-piloted as well as partly autonomous vehicles on roads, railways and in the air. These highly dynamic wireless communication channels are characterized by rapidly changing channel statistics. In this paper we present the first fully mobile multi-node vehicular wireless channel sounding system, which is capable of simultaneously capturing multiple channel frequency responses, ensuring that measurement conditions are identical for all observed links. We use it to analyze road scenarios with multiple vehicles and a large obstructing double-decker bus. The empirical measurement data is used to parametrize a model for the large obstructing vehicle within a geometry-based stochastic channel model. We compare the time-variant channel statistics obtained from our channel model with the ones from the measurement campaign. By means of a channel emulator we obtain the packet error rates of commercial modems for the measured and the simulated wireless communication channels and compare them, in order to validate the model at the link level. We find that the path loss, the root mean square (RMS) delay spread, and the RMS Doppler spread deviate by less than 3.6 dB, 78 ns, and 52 Hz, respectively, for 80% of the total simulation duration. The PER obtained from measured data is within the maximum and minimum bounds of our model for 86% of the simulation duration.
Life skills teachers teaching approach of the learning process in class

Approaches and methods of teaching and learning ( P & P ) are constantly changing . Recent developments show that the learning -oriented students are prime dvelopmention with a major radikal. Duties of an instructor or teacher is to facilitate students' learning . To fulfill this task , the instructor or teacher should not only be able to provide an excellent learning environment and harmonious , but they also create effective teaching . This means that teachers should create a learning environment that can stimulate student interest and always think about the welfare and needs. In the learning sessions, teachers are often faced with students who differ in their abilities. This requires the expertise of teachers to identify teaching and learning strategies. This means that the teacher can determine the approach, choosing methods and set specific techniques appropriate to the development and abilities of students. The chosen strategy, as well as potential influenced students to learn actively, it should also be able to help to analyze the concept or idea and be able to impress students and can produce a meaningful learning. Teachers teaching is the most important agent in determining the level of student achievement. This study focused on the type and method of teaching and its impact on student achievement in the subject Living Skills of the Form Two students of SMK Sri Gading. Questionnaires were used as instruments in this study. In this study, Spearman correlation test is used to measure the association between teaching approach with student achievement. Results of this study show that teachers of Form Two Life Skills teaching approach problem solving in the process of teaching and learning. The results also showed that they are also engaged in an inductive approach to teaching. The mean value is at a high valuation. However, in terms of comparison of the two approaches, a small difference in making sense of the process of teaching and learning Two Living Skills teacher at SMK Sri Gading, Batu Pahat, Johor, the two approaches used in classroom teaching. © 2014 Elixir All rights reserved ARTICLE INF O Articl e h istory: Received: 11 November 2013; Received in revised form: 19 December 2013; Accepted: 31 December 2013;
CuO nanostructures: facile synthesis and applications for enhanced photodegradation of organic compounds and reduction of p-nitrophenol from aqueous phase

1D CuO nanorods and 2D CuO nanosheets were synthesized for the first time using amino acids, namely L-lysine and L-glycine, by a microwave assisted green synthetic route. The amino acids act as a good complexing and capping agent in the synthesis of CuO nanoparticles. L-Lysine mediated synthesis leads to the formation of CuO nanorods having an average diameter of 30 nm, while L-glycine assisted synthesis leads to the formation of CuO nanosheets with dimensions of 300–600 nm length, 200 nm width and 30–60 nm thickness. Hence, the morphology and size of the CuO nanoparticles can be varied by changing the amino acids, with other parameters remaining unaffected. CuO nanorods and CuO nanosheets were characterized by FTIR, XRD, TEM, SAED and UV-visible spectroscopy. XRD, FTIR and SAED reveal the monoclinic phase of CuO nanoparticles. Absorption spectra of CuO nanorods and nanosheets show a broad absorption band around 380 nm and 383 nm, respectively, due to surface plasmon absorbance of CuO. A clear blue shift in the band gap energy of synthesized CuO nanorods was observed from CuO nanosheets, with a decrease in particle dimension due to the quantum effect. The catalytic activity of synthesized CuO nanorods and CuO nanosheets was studied for the reduction of p-nitrophenol to p-aminophenol. The results showed an enhanced catalytic potential of 1D CuO nanorods as compared with that of 2D CuO nanosheets. The photocatalytic activity of synthesized CuO nanoparticles was also evaluated for the degradation of two different toxic dyes, namely methylene blue and eosin Y, under solar irradiation. The degradation products were analyzed and a mechanistic pathway for the degradation is proposed.
It is All in the Wrist: Wearable Sleep Staging in a Clinical Population versus Reference Polysomnography

Purpose There is great interest in unobtrusive long-term sleep measurements using wearable devices based on reflective photoplethysmography (PPG). Unfortunately, consumer devices are not validated in patient populations and therefore not suitable for clinical use. Several sleep staging algorithms have been developed and validated based on ECG-signals. However, translation from these techniques to data derived by wearable PPG is not trivial, and requires the differences between sensing modalities to be integrated in the algorithm, or having the model trained directly with data obtained with the target sensor. Either way, validation of PPG-based sleep staging algorithms requires a large dataset containing both gold standard measurements and PPG-sensor in the applicable clinical population. Here, we take these important steps towards unobtrusive, long-term sleep monitoring. Methods We developed and trained an algorithm based on wrist-worn PPG and accelerometry. The method was validated against reference polysomnography in an independent clinical population comprising 244 adults and 48 children (age: 3 to 82 years) with a wide variety of sleep disorders. Results The classifier achieved substantial agreement on four-class sleep staging with an average Cohen’s kappa of 0.62 and accuracy of 76.4%. For children/adolescents, it achieved even higher agreement with an average kappa of 0.66 and accuracy of 77.9%. Performance was significantly higher in non-REM parasomnias (kappa = 0.69, accuracy = 80.1%) and significantly lower in REM parasomnias (kappa = 0.55, accuracy = 72.3%). A weak correlation was found between age and kappa (ρ = −0.30, p<0.001) and age and accuracy (ρ = −0.22, p<0.001). Conclusion This study shows the feasibility of automatic wearable sleep staging in patients with a broad variety of sleep disorders and a wide age range. Results demonstrate the potential for ambulatory long-term monitoring of clinical populations, which may improve diagnosis, estimation of severity and follow up in both sleep medicine and research.
Correlation Between Calcification Characteristics of Carotid Atherosclerotic Plaque and Plaque Vulnerability

Purpose To investigate the relationship between calcification characteristics of carotid atherosclerotic plaque and lipid rich necrotic core (LRNC) and intraplaque hemorrhage (IPH). Methods Patients with severe carotid stenosis undergoing carotid endarterectomy (CEA) were selected. Ultrasound and CT angiography (CTA) were performed to evaluate the calcification characteristics of the plaque before the surgery. Results A total of 142 patients were included and 142 pathological specimens of postoperative plaque were obtained accordingly. There were 78 plaques (54.9%) with LRNC and 41 (28.9%) with IPH. The plaque with LRNC had higher calcification rate (93.6%) compared with the plaque with IPH (87.8%). LRNC was often found in multiple calcification (P = 0.003) and mixed type calcification (P = 0.001). Multiple calcification was more likely to combine with IPH (P = 0.008), while simple basal calcification was not likely to combine IPH (P = 0.002). Smaller granular calcification was more likely to be associated with IPH (P < 0.05). In multivariate regression analysis of IPH and calcification characteristics, simple basal calcification was still a protective factor for IPH (OR, 0.25; 95% CI, 0.09–0.66; P = 0.005), while multiple calcification was closely related to the occurrence of IPH (OR, 3.58; 95% CI, 1.49–8.61; P = 0.004). Conclusion Calcification characteristics of carotid atherosclerotic plaques are closely related to the vulnerability of plaques, especially multiple calcification and mixed type calcification.
Foot Involvement as the First Manifestation in Rheumatoid Arthritis Patients in Lahore

Objective The objective of this study was to determine the involvement of the foot as the first manifestation in rheumatoid arthritis (RA). Methods This study was conducted on 100 patients who presented to the outpatient department of the Rheumatology Department at Fatima Memorial Hospital and College of Medicine and Dentistry in Lahore, Pakistan. The period of this cross-sectional study was three months - from October 2017 to December 2017. One hundred patients aged more than 16 years, who were diagnosed as cases of RA with foot involvement, and with a disease duration of less than two years (to minimize recall bias), were enrolled for the study. Results Out of the 100 patients, 20% were male and 80% were female. The mean age of the study population was 41.16 ± 12.343 years. Foot Involvement as the first manifestation was noted in 29 (29%) of the cases. The pattern of foot involvement shows a 59% forefoot involvement, 27% hindfoot involvement, and 14% midfoot involvement. Walking difficulty was most common in forefoot involvement (71.42% of cases), followed by hindfoot involvement (20% of cases), and least common in midfoot involvement (8.57% of cases) (p=0.0001). Conclusion Foot involvement as the first manifestation is quite common in RA and should not be ignored, especially in patients with large joint involvement sparing the hands.
Redistribution of Elements in Microbial Biomass in the Process of Silver and Gold Nanoparticles Synthesis Studied by Neutron Activation Analysis

Reactor neutron activation analysis was applied to characterize the elemental content of a microbial biomass in the process of synthesis of silver and gold nanoparticles from silver nitrate and chloroauric acid solutions. It was established that this process is accompanied by redistribution of some essential elements such as Ca, Cl, Fe, K, Mg, Mn, Na, P, U, Zn in microbial biomass both in case of different concentration loadings of silver and gold in aqueous solutions of silver nitrate and chloroauric acid, respectively, and in case of different incubation times. The role of cell surface adsorption in the formation of nanoparticles is discussed
A novel proline-rich M-superfamily conotoxin that can simultaneously affect sodium, potassium and calcium currents

Abstract Background Conotoxins have become a research hotspot in the neuropharmacology field for their high activity and specificity in targeting ion channels and neurotransmitter receptors. There have been reports of a conotoxin acting on two ion channels, but rare reports of a conotoxin acting on three ion channels. Methods Vr3a, a proline-rich M-superfamily conotoxin from a worm-hunting Conus varius, was obtained by solid-phase synthesis and identified by mass spectrometry. The effects of synthesized Vr3a on sodium, potassium and calcium currents were tested on rat DRG cells by patch clamp experiments. The further effects of Vr3a on human Cav1.2 and Cav2.2 currents were tested on HEK293 cells. Results About 10 μM Vr3a has no effects on the peak sodium currents, but can induce a ~10 mV shift in a polarizing direction in the current-voltage relationship. In addition, 10 μM Vr3a can increase 19.61 ± 5.12% of the peak potassium currents and do not induce a shift in the current-voltage relationship. An amount of 10 μM Vr3a can inhibit 31.26% ± 4.53% of the peak calcium currents and do not induce a shift in the current-voltage relationship. The IC50 value of Vr3a on calcium channel currents in rat DRG neurons is 19.28 ± 4.32 μM. Moreover, 10 μM Vr3a can inhibit 15.32% ± 5.41% of the human Cav1.2 currents and 12.86% ± 4.93% of the human Cav2.2 currents. Conclusions Vr3a can simultaneously affect sodium, potassium and calcium currents. This novel triple-target conotoxin Vr3a expands understanding of conotoxin functions.
Trial Tibial Inserts May Result in Different Knee Kinematics from Final Poly Inserts in Total Knee Arthroplasty

Introduction Trialling is a key step in total knee arthroplasty (TKA) and helps the surgeon assess for adequate balancing, range of motion, and stability. Despite this, there are no studies investigating knee kinematics when using trial versus final polyethylene tibial inserts. Materials and Methods Fourteen fresh frozen cadaveric specimens were cycled in a VIVO joint motion simulator. Using both simple compression and simulated muscle loads, joints were tested after TKA with a trial insert or a final tibial poly insert. Anterior/posterior (AP), internal/external (IE), and varus/valgus (VV) kinematics and laxities were analyzed. Results Knees with trial poly inserts had significantly greater AP hysteresis (difference between flexion and extension motion) than those with final poly inserts (p=0.001). There was no significant difference in IE (p=0.563) or VV (p=0.580) hysteresis. There was no difference in AP, IE, or VV motion or laxities when considering the flexion path alone. Prosthetic joints followed different paths in flexion versus extension. Conclusion While trial tibial inserts impart valuable information, they may not accurately reproduce the same joint kinematics as final inserts. Balancing of the knee at specific degrees of flexion may depend on the path taken to get there.
Prognostic Value of c-MYC Expression in Patients with Peripheral Neuroblastic Tumors

Objective Neuroblastic tumors are the most common solid tumors in children. The aim of this study was to explore the prognostic value of immunostaining for cellular-myelocytomatosis viral oncogene (c-MYC) expression in patients with peripheral neuroblastic tumors (NTs). Methods A retrospective study was conducted to compare the expression of c-MYC detected by immunohistochemistry and v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN) by fluorescence in situ hybridization among 177 cases of NTs and determine the associations of c-MYC and MYCN with the clinical stages, morphological types, and survival rates of NTs. Results The cases positive for c-MYC were mainly the favorable histology type in stage 3 or 4 with a poor NT prognosis, but no morphological changes related to the poor prognosis were observed in their samples under a microscope. The cases with positive c-MYC expression did not overlap those with MYCN amplification. Conclusion Positive c-MYC expression portends a poor prognosis in patients with NTs.
Hepatitis B virus genetic heterogeneity and drug resistance among jaundiced patients at Coast General Teaching and Referral Hospital, Mombasa County, Kenya

Objectives: Hepatitis B virus (HBV) infection and emergence of drug resistance have remained one of the major public health puzzles. This study determined circulating HBV genotypes and nucleoside analog resistance to provide information in choosing the best therapy. Methods: A cross-sectional study was conducted among jaundiced patients visiting Coast General Teaching and Referral Hospital during the period between February and August 2018. A total of 222 patients were recruited and screened for HBsAg following the ethical procedure. Viral DNA was extracted from positive samples, partial HBV-pol gene amplified, and directly sequenced and analyzed using web-based software prediction to genotypic resistance mutations. Results: Forty-seven (21.2%) of the 222 patients tested positive for HBV. Of the 45 samples successfully sequenced, 12 (26.4%) had drug resistance. Six patients (13.3%) had rtV173L, rtL180M, and rtM204V mutations; five subjects (11.1%) with rtL180M and rtM204V while 1 patient (2.2%) had rtM204V mutations. Therefore, all patients had cross-resistance to lamivudine and entecavir. Phylogenetic analysis revealed that HBV genotype A1 35 (74.5%) was predominant. HBV genotypes A3, B, and C2 each occurred once (0.02%). In addition, existence of new HBV genotypes A3, B, and C2 1 (0.02%) in the country was also detected. Conclusion: Findings suggest that HBV-infected patients should not be put on lamivudine monotherapy. These patients should be on a combination therapy; tenofovir plus lamivudine or emtricitabine to prevent emergence of drug resistance variants. In addition, HBV genotype A1 remains the most predominant genotype in this region. The detected new genotypes variants indicate a possible existence of 0.02% circulation within the population.