Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of Poisson, logit, and linear models for genetic analysis of clinical mastitis in Norwegian Red cows.

Clinical mastitis is typically coded as presence/absence during some period of exposure, and records are analyzed with linear or binary data models. Because presence includes cows with multiple episodes, there is loss of information when a count is treated as a binary response. The Poisson model is designed for counting random variables, and although it is used extensively in epidemiology of mastitis, it has rarely been used for studying the genetics of mastitis. Many models have been proposed for genetic analysis of mastitis, but they have not been formally compared. The main goal of this study was to compare linear (Gaussian), Bernoulli (with logit link), and Poisson models for the purpose of genetic evaluation of sires for mastitis in dairy cattle. The response variables were clinical mastitis (CM; 0, 1) and number of CM cases (NCM; 0, 1, 2, .). Data consisted of records on 36,178 first-lactation daughters of 245 Norwegian Red sires distributed over 5,286 herds. Predictive ability of models was assessed via a 3-fold cross-validation using mean squared error of prediction (MSEP) as the end-point. Between-sire variance estimates for NCM were 0.065 in Poisson and 0.007 in the linear model. For CM the between-sire variance was 0.093 in logit and 0.003 in the linear model. The ratio between herd and sire variances for the models with NCM response was 4.6 and 3.5 for Poisson and linear, respectively, and for model for CM was 3.7 in both logit and linear models. The MSEP for all cows was similar. However, within healthy animals, MSEP was 0.085 (Poisson), 0.090 (linear for NCM), 0.053 (logit), and 0.056 (linear for CM). For mastitic animals the MSEP values were 1.206 (Poisson), 1.185 (linear for NCM response), 1.333 (logit), and 1.319 (linear for CM response). The models for count variables had a better performance when predicting diseased animals and also had a similar performance between them. Logit and linear models for CM had better predictive ability for healthy cows and had a similar performance between them.
Performance evaluation of a Pedestrian Navigation System based on an objective experimental method

The ability to estimate the distance covered and the orientation of a person, regardless from where he or she is located, is an important aspect in various research areas and in particular in Pedestrian Navigation Systems (PNS) for emergency responders. In this paper we present a PNS based on a wearable wireless device attached to the instep of the pedestrian. The implemented real time algorithm, is able to identify pedestrian's strides, estimating theirs length and direction by using information provided from an embedded Inertial Measurement Unit (IMU). The proposed device is also equipped with MicroSD slot and Bluetooth module for data storage and for sending information in real time. The proposed system has been tested through an objective experimental method in which ten volunteers were walking along three different tracks, five times each, keeping the IMU attached to the instep. In the first trial subjects walked along a straight path that is 90m long, in the second they walked twice along a rectangular path with long side equal to 15m and short side equal to 7.5m and in the last they walked 400m along a standard athletics track. For each test we computed absolute and average error. The results show that the average error is 3.52% for the straight track, 1.09% for the rectangular track and 3.71% for the elliptic track.
An Experience with Auricular Free Flap Epiglottis Reconstruction after Supraglottic Laryngectomy

A total laryngectomy was once the treatment of choice in the majority of patients with laryngeal cancer. Horizontal partial laryngectomy has recently become an option for supraglottic tumors. This approach theoretically preserves both the voice and swallowing function. Surgical reconstruction after partial laryngectomy remains a challenge because of the high risk of postoperative complications such as aspiration and abnormal swallowing.1 Primary closure or local techniques lead to a high risk of chronic food aspiration and pulmonary damage in up to 80% of the patients.2 An idealmethod for the reconstructionof the entire epiglottis and part of the tongue base would utilize tissues that are native to the area, highly viable, convenient to the surgeon, and expendable to the patient. This tissue should be a composite containing both epithelium and skeletal support. Here, we describe the surgical procedure for reconstructing the epiglottis.
Quantifying the contribution of genetic variants for survival phenotypes

Particularly in studies based on population representative samples, it is of major interest what impact a genetic variant has on the phenotype of interest, which cannot be answered by mere association estimates alone. One possible measure for quantifying the phenotype's variance explained by the genetic variant is R2. However, for survival outcomes, no clear definition of R2 is available in the presence of censored observations. We selected three criteria proposed for this purpose in the literature and compared their performance for single nucleotide polymorphism (SNP) data through simulation studies and for mortality data with candidate SNPs in the general population‐based KORA cohort. The evaluated criteria were based on: (1) the difference of deviance residuals, (2) the variation of individual survival curves, and (3) the variation of Schoenfeld residuals. Our simulation studies included various censoring and genetic scenarios. The simulation studies revealed that the deviance residuals' criterion had a high dependence on the censoring percentage, was generally not limited to the range [0; 1] and therefore lacked interpretation as a percentage of explained variation. The second criterion (variation of survival curves) hardly reached values above 60%. Our requirements were best fulfilled by the criterion based on Schoenfeld residuals. Our mortality data analysis also supported the findings in simulation studies. With the criterion based on Schoenfeld residuals, we recommend a powerful and flexible tool for genetic epidemiological studies to refine genetic association studies by judging the contribution of genetic variants to survival phenotype. Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.
Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila

Deletions of specific DNA sequences are known to occur in Tetrahymena thermophila as a developmentally regulated process. Deletions of a particular region (region M) were previously shown to be of two alternative sizes, 0.6 or 0.9 kilobases (kb) (C.F. Austerberry, C.D. Allis, and M.-C. Yao, Proc. Natl. Acad. Sci. USA 81: 7383-7387). In this study, the nucleotide sequences for both deletions were determined. These two deletions share the same right junction, but their left junctions are 0.3 kb apart. An 8-base-pair (bp) sequence is present at both junctions of the 0.6-kb deletion, but only 5 bp of this direct repeat are present at the left junction of the 0.9-kb deletion. Further comparison revealed a common 10-bp sequence near each of the two left junctions and a similar sequence in inverted orientation near the right junction. These sequences may play a role in the developmental regulation of the deletion process.
Hardening techniques for MRAM-based non-volatile storage cells and logic

Magnetic RAM (MRAM) is considered as a promising non-volatile memory technology for aerospace and avionic electronics thanks to its intrinsic hardness to radiation. Data is stored on the spin direction “up” and “down” of electrons instead of positive and negative charge. However, MRAM-based non-volatile storage cells and logic circuits are vulnerable to Single Event Effects (SEE) due to their CMOS peripheral circuits. Hardening techniques to mitigate SEE are presented in this paper. A new design of Radhard MRAM latch is firstly presented. TMR technique is then implemented on Configurable Logic Block to mitigate SET on data paths. By using 65nm design kit and an MRAM compact model, hybrid simulations have been done to demonstrate the radiation hardness.
Size-Scalable Content-Based Histopathological Image Retrieval From Database That Consists of WSIs

Content-based image retrieval (CBIR) has been widely researched for histopathological images. It is challenging to retrieve contently similar regions from histopathological whole slide images (WSIs) for regions of interest (ROIs) in different size. In this paper, we propose a novel CBIR framework for database that consists of WSIs and size-scalable query ROIs. Each WSI in the database is encoded into a matrix of binary codes. When retrieving, a group of region proposals that have similar size with the query ROI are firstly located in the database through an efficient table-lookup approach. Then, these regions are ranked by a designed multi-binary-code-based similarity measurement. Finally, the top relevant regions and their locations in the WSIs as well as the corresponding diagnostic information are returned to assist pathologists. The effectiveness of the proposed framework is evaluated on a fine-annotated WSI database of epithelial breast tumors. The experimental results have proved that the proposed framework is effective for retrieval from database that consists of WSIs. Specifically, for query ROIs of 4096 $\times$ 4096 pixels, the retrieval precision of the top 20 return has reached 96% and the retrieval time is less than 1.5 s.
Rapid detection of coliforms in drinking water of Arak city using multiplex PCR method in comparison with the standard method of culture (Most Probably Number).

OBJECTIVE To analyse molecular detection of coliforms and shorten the time of PCR. METHODS Rapid detection of coliforms by amplification of lacZ and uidA genes in a multiplex PCR reaction was designed and performed in comparison with most probably number (MPN) method for 16 artificial and 101 field samples. The molecular method was also conducted on isolated coliforms from positive MPN samples; standard sample for verification of microbial method certificated reference material; isolated strains from certificated reference material and standard bacteria. The PCR and electrophoresis parameters were changed for reducing the operation time. RESULTS Results of PCR for lacZ and uidA genes were similar in all of standard, operational and artificial samples and showed the 876 bp and 147 bp bands of lacZ and uidA genes by multiplex PCR. PCR results were confirmed by MPN culture method by sensitivity 86% (95% CI: 0.71-0.93). Also the total execution time, with a successful change of factors, was reduced to less than two and a half hour. CONCLUSIONS Multiplex PCR method with shortened operation time was used for the simultaneous detection of total coliforms and Escherichia coli in distribution system of Arak city. It's recommended to be used at least as an initial screening test, and then the positive samples could be randomly tested by MPN.
Induction of cap-independent BiP (hsp-3) and Bcl-2 (ced-9) translation in response to eIF4G (IFG-1) depletion in C. elegans

During apoptosis, activated caspases cleave the translation initiation factor eIF4G. This cleavage disrupts cap-dependent mRNA translation initiation within the cell. However, a specific subset of mRNAs can still be recruited for protein synthesis in a cap-independent manner by the residual initiation machinery. Many of these mRNAs, including cell death related mRNAs, contain internal ribosome entry sites (IRESes) that promote their enhanced translation during apoptosis. Still other mRNAs have little dependence on the cap recognition mechanism. The expression of the encoded proteins, both anti- and pro-apoptotic, allows for an initial period of attempted cell survival, then commitment to cell death when damage is extensive. In this study we address the translational regulation of the stress and apoptosis-related mRNAs in C. elegans: BiP (hsp-3) (hsp-4), Hif-1 (hif-1), p53 (cep-1), Bcl-2 (ced-9) and Apaf-1 (ced-4). Altered translational efficiency of these messages was observed upon depletion of cap-dependent translation and induction of apoptosis within the C. elegans gonad. Our findings suggest a physiological link between the cap-independent mechanism and the enhanced translation of hsp-3 and ced-9. This increase in the efficiency of translation may be integral to the stress response during the induction of physiological apoptosis.
Evaluation of Discourse Relation Annotation in the Hindi Discourse Relation Bank

We describe our experiments on evaluating recently proposed modifications to the discourse relation annotation scheme of the Penn Discourse Treebank (PDTB), in the context of annotating discourse relations in Hindi Discourse Relation Bank (HDRB). While the proposed modifications were driven by the desire to introduce greater conceptual clarity in the PDTB scheme and to facilitate better annotation quality, our findings indicate that overall, some of the changes render the annotation task much more difficult for the annotators, as also reflected in lower inter-annotator agreement for the relevant sub-tasks. Our study emphasizes the importance of best practices in annotation task design and guidelines, given that a major goal of an annotation effort should be to achieve maximally high agreement between annotators. Based on our study, we suggest modifications to the current version of the HDRB, to be incorporated in our future annotation work.
Recognition of Partially Occluded Objects Using B-tree Index Structure: An Efficient and Robust Approach

This paper presents a novel method for recognizing partially occluded objects. The proposed method uses corner points and their spatial relationship perceived through the application of Triangular Spatial Relationship (TSR) [5] by considering three successive corner points at a time. The perceived TSR among corner points are used to create a model object-base using B-tree, an efficient multilevel indexing scheme. The matched sequence is preserved in a two-dimensional matrix called status matrix. Experimental results, on real images of varying complexity of a reasonably large database of objects have established the robustness of the method.
Diffuse thalamic projection system in monkey.

In 1942, Dempsey and Morison (4–6, 24) discovered in cats a thalamic system which upon direct repetitive stimulation evoked recruiting wave responses in broad areas of the cortex. Evidence was presented that the physiological counterpart of this response to stimulation was burst or spindle activity recorded from the cortex of cats under surgical barbiturate anesthesia. Interest in the mechanism of the recruiting response has been heightened by proposals concerning its functional significance, the most discussed being Jasper’s suggestion that it represents the basis for petit mal epilepsy (15, 17, 18). In the cat, sites of origin for the diffuse thalamic projection system have been found to be the centre median and intralaminar nuclei (24), as well as the ventralis anterior and rostral pole of the reticular nucleus (33). These component nuclei act as a functional unit for, on repetitive stimulation of any one of them, recruiting waves can be recorded from all (33). The mediation of recruiting to the cortex has been suggested to occur either through the reticular nucleus throughout its extent (17, 30, 31) or by way of the rhinencephalon (31). It has been shown (33), however, that the principal transmission of recruitment to the cortex occurs through connections with the thalamic associational nuclei, although possibly some direct connections also exist between the recruiting nuclei of origin and the cortex. In accordance with these findings, the cortical responses were found to be limited to areas having projections from these association nuclei, with identical cortical localization irrespective of which recruiting nucleus was stimulated (33). The foregoing evidence in the cat suggested that the diffuse projection system is organized for mass thalamic influence on associational cortex (33). However, because of the relatively poor differentiation of the cat’s associational nuclei and cortex, in the present study more conclusive evidence was sought in the macaque, which, with its higher order of both cortical and sub-cortical development, more closely simulates the human brain.
COFFEE: A Context-Free Protocol for Stimulating Data Forwarding in Wireless Ad Hoc Networks

Reputation based and credit-exchange based approaches have been studied extensively to enforce cooperation among non-cooperative nodes in wireless ad hoc networks. Most of the existing solutions are fundamentally context-based ones, which need to accurately identify selfish behaviors, securely maintain the context, and appropriately punish the selfish nodes. These requirements are extremely difficult to satisfy if not impossible. From a completely new angle, this paper proposes a context-free protocol, COFFEE, to enforce cooperation among selfish nodes, which has the ability to transmit a packet over the path successfully without the dependency on the information of other packets' transmission. Considering that every node in the network is rational, during the packet forwarding stage, if the intermediate nodes can not clearly tell whether the packet is destined to them or not, they can not simply drop the packet. Thus, in our proposed COFFEE protocol, through introducing several techniques, for any packet received by any node, the node thinks the packet could be destined to it and forwards the packet to find out the answer. Detailed analysis and performance evaluation have been conducted to demonstrate the effectiveness of the proposed protocol.
Simulated Satisfaction of Coverage Criteria on UML State Machines

UML state machines are widely used as test models in model-based testing. Coverage criteria are applied to them, e.g. to measure a test suite's coverage of the state machine or to steer automatic test suite generation based on the state machine. The model elements to cover as described by the applied coverage criterion depend on the structure of the state machine. Model transformations can be used to change this structure. In this paper, we present semantic-preserving state machine transformations that are used to influence the result of the applied coverage criteria. The contribution is that almost every feasible coverage criterion that is applied to the transformed state machine can have at least the same effect as any other feasible, possibly stronger coverage criterion that is applied to the original state machine. We introduce simulated satisfaction as a corresponding relation between coverage criteria. We provide formal definitions for coverage criteria and use them to prove the correctness of the model transformations that substantiate the simulated satisfaction relations. The results of this paper are especially important for model-based test generation tools, which are often limited to satisfy a restricted set of coverage criteria.
Plume‐driven plumbing and crustal formation in Iceland

[1] Through combination of surface wave and body wave constraints we derive a three-dimensional (3-D) crustal S velocity model and Moho map for Iceland. It reveals a vast plumbing system feeding mantle plume melt into upper crustal magma chambers where crustal formation takes place. The method is based on the partitioned waveform inversion to which we add additional observations. Love waves from six local events recorded on the HOTSPOT- SIL networks are fitted, Sn travel times from the same events measured, previous observations of crustal thickness are added, and all three sets of constraints simultaneously inverted for our 3-D model. In the upper crust (0–15 km) an elongated low-velocity region extends along the length of the Northern, Eastern and Western Neovolcanic Zones. The lowest velocities (−7%) are found at 5–10 km below the two most active volcanic complexes: Hekla and Bardarbunga-Grimsvotn. In the lower crust (>15 km) the low-velocity region can be represented as a vertical cylinder beneath central Iceland. The low-velocity structure is interpreted as the thermal halo of pipe work which connects the region of melt generation in the uppermost mantle beneath central Iceland to active volcanoes along the neovolcanic zones. Crustal thickness in Iceland varies from 15–20 km beneath the Reykjanes Peninsula, Krafla and the extinct Snaefellsnes rift zone, to 46 km beneath central Iceland. The average crustal thickness is 29 km. The variations in thickness can be explained in terms of the temporal variation in plume productivity over the last ∼20 Myr, the Snaefellsnes rift zone being active during a minimum in plume productivity. Variations in crustal thickness do not depart significantly from an isostatically predicted crustal thickness. The best fit linear isostatic relation implies an average density jump of 4% across the Moho. Rare earth element inversions of basalt compositions on Iceland suggest a melt thickness (i.e., crustal thickness) of 15–20 km, given passive upwelling. The observed crustal thickness of up to 46 km implies active fluxing of source material through the melt zone by the mantle plume at up to 3 times the passive rate.
Optical Character Recognition for Cursive Handwriting

A new analytic scheme, which uses a sequence of image segmentation and recognition algorithms, is proposed for the off-line cursive handwriting recognition problem. First, some global parameters, such as slant angle, baselines, stroke width and height, are estimated. Second, a segmentation method finds character segmentation paths by combining gray-scale and binary information. Third, a hidden Markov model (HMM) is employed for shape recognition to label and rank the character candidates. For this purpose, a string of codes is extracted from each segment to represent the character candidates. The estimation of feature space parameters is embedded in the HMM training stage together with the estimation of the HMM model parameters. Finally, information from a lexicon and from the HMM ranks is combined in a graph optimization problem for word-level recognition. This method corrects most of the errors produced by the segmentation and HMM ranking stages by maximizing an information measure in an efficient graph search algorithm. The experiments indicate higher recognition rates compared to the available methods reported in the literature.
Polyp Detection in Colonoscopy Video using Elliptical Shape Feature

Early detection of polyps and cancers is one of the most important goals of colonoscopy. Computer-based analysis of video files using texture features, as has been proposed for polyps of the stomach and colon, has two major limitations: this method uses a fixed size analysis window and relies heavily on a training set of images for accuracy. To overcome these limitations, we propose a new technique focusing on shape instead of texture in this paper. The proposed polyp region detection method is based on the elliptical shape that is common for nearly all small colon polyps.
Role competencies for a fieldwork educator.

Purpose: These role competencies have been developed to assist educational programs in determining and/or evaluating the typical responsibilities for a fieldwork educator associated with an occupational therapy program. The competencies are based on the American Occupational Therapy Association’s Standards for Continuing Competence. These role competencies are statements describing the typical values, knowledge, skills, and responsibilities that are needed to be successful in the role of a fieldwork educator. The competencies are general statements, as specific competencies may not apply to all situations. Each competency may be modified and should be considered guidelines for institutions or educational settings.