Miracle-dz/UniFAR-FTUs huggingface dataset:
Transfer of Cornus florida and C. kousa Simple Sequence Repeats to Selected Cornus (Cornaceae) Species

Cross-species transferability of simple sequence repeats (SSRs) is common and allows SSRs isolated from one species to be applied to closely related species, increasing the use of previously isolated SSRs. The genus Cornus consists of 58 species that are ecologically and economically important. SSRs have previously been isolated from C. florida and C. kousa. In this study, 36 SSRs were tested on taxa from 18 Cornus species and hybrids for cross-species transferability and genetic diversity was calculated for each locus using polymorphism information content (PIC). Cross-species transferability of SSR loci was higher in more closely related species and PIC values were high. Evidence was found for conserved primer sites as determined by the amplification of SSR loci in the taxa examined. Polymerase chain reaction products were cloned and sequenced for three SSR loci (CF48, CF59, and CF124) and all individuals sequenced contained the appropriate repeat. Phylogenetic relationships of 14 Cornus species were inferredusingnucleotidesequencesofSSRlocusCF48.Themostparsimonioustree resultingfromthisanalysiswasin concordance with phylogenies based on matK and internal transcribed spacer sequences. The SSR loci tested in this study will be useful in future breeding, population, and genetic studies within Cornus.
Robust multilingual parsing using island grammars

Any attempt at automated software analysis or modification must be preceded by a comprehension step, i.e. parsing. This task, while often considered straightforward, can in fact be very challenging for some source code. Files that make up web applications serve as an example of such difficult-to-parse artifacts, for two reasons. First, these files often contain several programming languages at once, sometimes with widely varying syntaxes, and intermingled at the statement level. Second, the code routinely contains syntax errors. Understanding such files calls for a robust parser that can handle multiple languages simultaneously.An approach to creating such a parser, based on the concept of island grammars, is presented here. Island grammars have been used in the past for robust parsing and lightweight analysis of software. Some of the features of these grammars make them uniquely fit for parsing multiple languages simultaneously.
Leprosy lesion recognition using convolutional neural networks

Leprosy, also known as Hansen's disease, is a debilitating and chronic bacterial infection. As per World Health Organization's report, there were 189,000 chronic cases of Leprosy in 2012 with 230,000 new diagnoses. Although curable at later stages, an early diagnosis prevents nerve involvement and the disabilities it incurs. The authors henceforth propose a Convolutional Neural Network based architecture for Leprosy lesion recognition. To train the network, authors use DermnetNz datasets along with web scraped images to achieve a best accuracy of 91.6% on a dataset split into 60% of training images, 20% of images are used for cross validation and 20% for testing.
Survival language learning syllabuses revisited: a customized functional-notional approach

Research on survival English syllabuses has been scarce in the last decades. There is nothing worse than the solitude of a teacher facing a course with such characteristics as continuous hesitations about the materials, activities and the learners' needs arise every now and then. Our contribution stems from Nation and Crabbe's article "A Survival Language Learning Syllabus for Foreign Travel" published in System in 1991, where a topic-based syllabus is proposed. The two-year experimental use of Nation and Crabbe's model, though successful, unveiled some shortcomings having to do with the inventory of situations and the lexical domain included therein. In the light of the limited period of instruction and the short-term benefits that these courses usually hold, a functional/ notional model has been designed for the purpose inasmuch as students seem to gain a
Low-power bootstrapped sample and hold circuit for analog-to-digital converters

In this paper, a modified low-power bootstrapped sample and hold (S/H) circuit is proposed. The effect of the proposed modified low-power bootstrapped sample and hold (S/H) circuit appears in the medium and high-frequency applications in which it reduces the power consumption without affecting the signal-to-noise and distortion ratio (SNDR). The proposed modified low-power bootstrapped sample and hold (S/H) circuit is based on eliminating the multiplier circuit which is responsible for keeping the gate-source voltage of the sampling transistor constant and replaced it with a PMOS transistor which performed the same job. In addition to that, it is based on using the transmission gate as the sampling transistors which avoid the degradation of the signal-to-noise and distortion ratio (SNDR). All the introduced bootstrapped sample and hold (S/H) circuits were simulated using 90nm CMOS technology on LT Spice IV. As a result, the proposed modified low-power bootstrapped sample and hold (S/H) circuit saves 70% to 92% of the power consumption compared with previous work reported in the literature with signal-to-noise and distortion ratio (SNDR) of 57 dB for 7 MHz input frequency signal.
Medical Equipment Utility Analysis based on Queuing Theory

To improve the efficiency of hospital, reduce patients’ waiting time, as well as meet patients’ satisfaction, the optimization of patients’ queuing system which is based on the knowledge of queuing theory has the practical significance in the use of medical equipments. Based on the relevant data of the usage of B- ultrasound in a hospital, the distribution model of queuing theory has been analyzed by the χ2 test of goodness of fit, then being able to describe the law of probability of queuing system in a scientific and exact way, and finally the application of the hospital instruments will be arranged in the most efficient way. The wish model can be set and decided by two indexes: one is the average time of patients’ waiting time in queuing system, the other is the free rate of medical equipments, and then the director can identify the best status of the model. This method, on one hand, can optimize the hospital service, improve the efficiency as well as supply the scientific evidence and reference for the director to arrange the material and human resources reasonably; on the other hand, it can find out a balance between patients and hospitals through system optimization. In this way, not only can short the waiting time, but also can save the human resources and materials of the hospital. The paper also provides a theoretical basis for hospital administrators to manage and optimize medical equipment.
Mobility-aware DASH for cost-optimal mobile multimedia streaming services

For multimedia streaming in mobile environments, video bitrate should be carefully determined and different channel quality and pricing in heterogeneous wireless networks (e.g., cellular and WiFi networks) need to be considered. In this work, we propose a new bitrate adaptation (BA) technique called mobility-aware dynamic adaptive streaming over HTTP (MDASH), in which a cellular data usage is minimized through a Markov Decision Process (MDP) framework. Preliminary simulation results are shown that MDASH can reduce 23% of the cellular data usage without any playback interruptions while minimizing the temporal variations in the video quality.
Acoustic Variation Conditioned by Prosody in English Motherese

The current study exploresacoustic variation induced by prosodic contexts in different speech styles,with a focus on motherese or child-directed speech (CDS). The patterns of variation in the acoustic expression of voicing contrast in English stops, and the role of prosodic factors in governing such variation are investigated in CDS. Prosody-induced acoustic strengthening reported from adult-directed speech (ADS)is examined in the speech data directed to infants at the one-word stage. The target consonants are collected from Utterance-initial and -medial positions, with or without focal accent. Overall, CDS shows that the prosodic prominence of constituents under focal accent conditions variesin the acoustic correlates of the stop laryngeal contrasts. The initial position is not found with enhanced acoustic values in the current study, which is similar to the finding from ADS (Choi, 2006 Cole et al, 2007). Individualized statistical results, however, indicate that the effect of accent on acoustic measures is not very robust, compared to the effect of accent in ADS. Enhanced distinctiveness under focal accent is observed from the limited subjects’ acoustic measures in CDS. The results indicate dissimilar strategies to mark prosodic structures in different speech styles as well as the consistent prosodic effect across speech styles. The stylistic variation is discussed in relation to the listener under linguistic development in CDS.
Peculiarities of the expression Р16ink4a under cervical intraepithelial neoplasia in women with reproductive disorders

We conducted comprehensive clinic-morphological study of 250 women with cervical intraepithelial neoplasia (CIN) with reproductive function disorders, of which in 157 (62, 8%) female patients was identified DNA of human papilloma virus (HPV) of high carcinogenic risk (HCR). We established the presence of HPV DNA in 62 female patients (56, 4 %) – under mild CIN, in 53 (61, 2%) – under moderate CIN, and 42 (77, 7%) – under sever CIN. The obtained results of immunohistochemical study indicate that the р16ink4a marker can be used as an additional criterion for the diagnosis of cervical intraepithelial neoplasia associated with papilloma viral infection and for the determination of the dysplastic process degree. Use of р16ink4a allows assessing the potential of dysplasia in relation to the development of cervical cancer and, consequently, to choose an adequate therapeutic tactics of this disease in women with infertility.
Increasing the environment-awareness of rake beamforming for directive acoustic sources

Speech signals captured by distant microphones in enclosures are typically deteriorated by reverberation and background noise. Commonly, the quality of the signals is enhanced applying delay and sum beamforming (or variants) to a microphone array. However, under particular conditions, the multi-path acoustic propagation leading to reverberation is not completely detrimental and can be used in a constructive way. In this direction, mirrored (virtual) microphones have been successfully applied in various research areas. In addition, the majority of naturally occurring sound sources, such as the human speaker, presents a certain degree of radiation directivity, which, coupled with data-independent beamforming, has been shown to slightly increase the captured speech quality. Building upon the concepts of environment awareness and the acoustic rake receiver, this paper investigates the use of mirrored microphones, associated to isolated and strong reflections, in combination with source directivity, to further improve the captured speech quality. Real-data gathered with a linear nested array, as well as simulated data, are used to test the proposed scheme, showing superior performance with respect to similar state of the art solutions.
Assessment of Iterative Closest Point Registration Accuracy for Different Phantom Surfaces Captured by an Optical 3D Sensor in Radiotherapy

An optical 3D sensor provides an additional tool for verification of correct patient settlement on a Tomotherapy treatment machine. The patient's position in the actual treatment is compared with the intended position defined in treatment planning. A commercially available optical 3D sensor measures parts of the body surface and estimates the deviation from the desired position without markers. The registration precision of the in-built algorithm and of selected ICP (iterative closest point) algorithms is investigated on surface data of specially designed phantoms captured by the optical 3D sensor for predefined shifts of the treatment table. A rigid body transform is compared with the actual displacement to check registration reliability for predefined limits. The curvature type of investigated phantom bodies has a strong influence on registration result which is more critical for surfaces of low curvature. We investigated the registration accuracy of the optical 3D sensor for the chosen phantoms and compared the results with selected unconstrained ICP algorithms. Safe registration within the clinical limits is only possible for uniquely shaped surface regions, but error metrics based on surface normals improve translational registration. Large registration errors clearly hint at setup deviations, whereas small values do not guarantee correct positioning.
Methods for Pattern Discovery in Unaligned Biological Sequences

Pattern discovery in biological sequences is the problem of ®nding patterns that are overrepresented in a set of unaligned DNA or protein sequences of related biological function. Such patterns could correspond to regions of the sequences responsible for the function itself, and could be used later for the functional annotation of newly determined sequences. Despite many studies, this problem can be considered far from being solved. The main dif®culty lies in the fact that signi®cant patterns can appear within each sequence with mutations, insertions or deletions of nucleotides or amino acids, without losing their biological function. This paper provides a survey of a number of existing pattern discovery algorithms, focusing both on the methods underlying them and their availability for the scienti®c community. INTRODUCTION In the last few years, the amount of biological data generated by the scienti®c community has grown exponentially, and a huge number of sequences are now available in several databases. Thus, the focus of many research projects has shifted from the generation of the data to their analysis, that is, the extraction of any kind of biological meaning from the sequences. Given a set of functionally related sequences, the main aim of patterndiscovery algorithms is to ®nd new and a priori unknown patterns that appear in every sequence, or at least in a signi®cant number of sequences, of the set. Such patterns could correspond to the regions of the sequences responsible for their function, and could be also used later for the functional annotation of newly determined sequences. From a computational point of view, the main dif®culty lies in the fact that the same pattern can appear within each sequence in a different and approximate form (ie with mutations, insertions or deletions of nucleotides or amino acids), keeping intact its biological function. The longer the patterns and the more degraded their occurrences, the harder (and slower) it is to ®nd them for patterndiscovery algorithms. A large number of different methods has been so far introduced, but we do not have yet good models or reliable algorithms that guarantee to ®nd all (or most of) the biologically meaningful patterns. This paper, without the claim of being exhaustive, provides a survey of a number of different approaches to the problem, presenting the main ideas underlying the methods and mentioning, when available, the software tools based on the different algorithms.
Experimental infection of mouse peritoneal mesothelium with scrub typhus rickettsiae: an ultrastructural study

The infection cycle of Rickettsia tsutsugamushi in mouse peritoneal mesothelial cells, observed late in the course of an established infection, intimately involved the host cell plasma membrane. Organisms multiplied in the cytoplasm, moved to the cell periphery, and acquired a host-membrane coat as they budded from the cell surface. Rickettsiae enveloped by this membrane entered other mesothelial cells, apparently by a phagocytic mechanism. Organisms escaped from the phagocytic vacuole as the vacuole membrane and host membrane coat disintegrated. Free rickettsiae replicated by binary fission in the cell cytoplasm. Rickettsial infection of mesothelial cells induced conspicuous cellular hypertrophy with increased numbers of unaltered cytoplasmic organelles.
Immunohistochemical expression of Type IV Collagen and Autocrine Motility Factor Receptor in Odontogenic Tumours.

BACKGROUND Autocrine motility factor receptor (AMFR) is a tumour motility stimulating protein secreted by tumour cells. The protein encoded by this gene is a glycosylated transmembrane protein and a receptor for autocrine motility factor. It has been known to play a role in progression of neoplastic lesions. Basement membranes are specialized extracellular matrices that serve as structural barriers as well as substrates for cellular interactions. The network of type IV collagen is thought to define the scaffold integrating other components such as laminins and perlecan into highly organized supramolecular architecture. The aim of this study was to determine and evaluate the immunohistochemical expression of Type IV Collagen and Autocrine motility factor receptor in odontogenic lesions. MATERIALS AND METHODS Immunohistochemical expression of Type IV Collagen and Autocrine motility factor receptor was evaluated in 31 odontogenic lesions, including unicystic ameloblastoma, multicystic ameloblastoma, keratocystic odontogenic tumour and ameloblastic carcinoma. Normal follicular tissue formed the control. RESULTS Maximum expression for Type IV Collagen was seen in multicystic ameloblastoma and minimum expression in keratocystic odontogenic tumour. The maximum expression of AMFR was seen in ameloblastic carcinoma and minimum expression in multicystic ameloblastoma. CONCLUSION The results of this study suggested an association of loss of expression of type IV Collagen with progression of lesion. AMFR expression was found to be associated with the aggressive potential of tumours.
Computer-aided optimization of DC/DC converters for automotive applications

This paper investigates computer-aided optimization of DC/DC converters, with a focus on converters for dual-voltage automotive electrical systems. A new CAD optimization approach based on Monte Carlo search methods is introduced which allows the design space to be rapidly explored in an automated fashion and the most optimal designs and design approaches to be identified. The optimization approach also allows the effects of variations in design specifications on the cost, weight, and volume of an optimized converter to be readily determined.
Regulation of Compound Leaf Development by PHANTASTICA in Medicago truncatula1[C][W][OPEN]

A MYB domain protein maintains petiole identity by repressing expression of a motor organ identity gene and promoting petiole and stipule development in Medicago truncatula. Plant leaves, simple or compound, initiate as peg-like structures from the peripheral zone of the shoot apical meristem, which requires class I KNOTTED-LIKE HOMEOBOXI (KNOXI) transcription factors to maintain its activity. The MYB domain protein encoded by the ASYMMETRIC LEAVES1/ROUGH SHEATH2/PHANTASTICA (ARP) gene, together with other factors, excludes KNOXI gene expression from incipient leaf primordia to initiate leaves and specify leaf adaxial identity. However, the regulatory relationship between ARP and KNOXI is more complex in compound-leafed species. Here, we investigated the role of ARP and KNOXI genes in compound leaf development in Medicago truncatula. We show that the M. truncatula phantastica mutant exhibited severe compound leaf defects, including curling and deep serration of leaf margins, shortened petioles, increased rachises, petioles acquiring motor organ characteristics, and ectopic development of petiolules. On the other hand, the M. truncatula brevipedicellus mutant did not exhibit visible compound leaf defects. Our analyses show that the altered petiole development requires ectopic expression of ELONGATED PETIOLULE1, which encodes a lateral organ boundary domain protein, and that the distal margin serration requires the auxin efflux protein M. truncatula PIN-FORMED10 in the M. truncatula phantastica mutant.
COHESION OF PROFESSIONAL WRITINGS AS FOUND IN THE JAKARTA POST

Coherence is a key concept for text comprehension and text clarity. One feature that contributes to coherence is cohesion which is realized in cohesive devices and metadiscourse markers. The current study is about cohesion in professional writings found in The Jakarta Post . Its purposes are to find out the cohesive devices and metadiscourse markers and to analyze how the cohesion significantly contributes to the coherence. The study is descriptive and qualitative in nature. The data are 4 professional writings taken from The Jakarta Post . The research results show that the average of the textual cohesion used in the professional writings is less than 50 %. It means that the textual cohesion is not sufficiently used. This also means that the cohesion used in the professional writings does not contribute so significantly to the texts’ coherence. Based on the conclusion above, it is suggested that the students be reminded the importance of textual cohesion to contribute coherence. The teacher should teach the students what textual and point-to-point cohesion is. Key words : cohesive devices, metadiscourse markers, textual cohesion, point-to-point cohesion
Carefully Appoximated Bayes Factors for Feature Selection in MaxEnt Models

Feature selection is essentially a model selection problem. If we take a frequentist maximum likelihood approach, we will, in the limit, select all features (unless, as is typical, we apply some sort of “early stopping” critereon). Additionally, basing the next feature to selected solely on standard measures such as likelihood gain, we fail to account for the variance of the estimate of this feature. In this note, I carefully derive an approximation to the Bayes factor in the feature/model selection problem for maximum entropy models. See [2] for an introduction to the use of maximum entropy models in the natural language processing domain. The advantages to using a Bayesian criterea for model selection are numerous, but the two strongest are that (a) it enables us to take into account uncertainty in likelihood when adding new features and (b) it allows us to decide when to stop adding features.
Identification and Analysis of Natural Killer Cells in Murine Nasal Passages

Background Natural killer (NK) cells in the upper respiratory airways are not well characterized. In the current study, we sought to characterize and functionally assess murine nasal NK cells. Methods Using immunohistochemistry and flow cytometry, we compared the nasal NK cells of Ncr1 GFP/+ knock-in mice, whose NK cells produced green fluorescent protein, with their splenic and pulmonary counterparts. In addition, we functionally analyzed the nasal NK cells of these mice in vitro. To assess the in vivo functions of nasal NK cells, C57BL/6 mice depleted of NK cells after treatment with PK136 antibody were nasally infected with influenza virus PR8. Results Immunohistochemical analysis confirmed the presence of NK cells in the lamina propria of nasal mucosa, and flow cytometry showed that these cells were of NK cell lineage. The expression patterns of Ly49 receptor, CD11b/CD27, CD62L and CD69 revealed that nasal NK cells had an immature and activated phenotype compared with that of their splenic and pulmonary counterparts. Effector functions including degranulation and IFN(interferon)-γ production after in vitro stimulation with phorbol 12-myristate-13-acetate plus ionomycin or IL(interleukin)-12 plus IL-18 were dampened in nasal NK cells, and the depletion of NK cells led to an increased influenza virus titer in nasal passages. Conclusions The NK cells of the murine nasal passage belong to the conventional NK cell linage and characteristically demonstrate an immature and activated phenotype. Despite their hyporesponsiveness in vitro, nasal NK cells play important roles in the host defense against nasal influenza virus infection.