Miracle-dz/UniFAR-FTUs huggingface dataset:
De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection

Pathogens like Puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. The interaction at molecular level between wheat and the pathogen is complex and less explored. The pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene Lr28). Four Serial Analysis of Gene Expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to Sequencing by Oligonucleotide Ligation and Detection, which generated a total of 165,767,777 reads, each 35 bases long. The reads were processed and multiple k-mers were attempted for de novo transcript assembly; 22 k-mers showed the best results. Altogether 21,345 contigs were generated and functionally characterized by gene ontology annotation, mining for transcription factors and resistance genes. Expression analysis among the four libraries showed extensive alterations in the transcriptome in response to pathogen infection, reflecting reorganizations in major biological processes and metabolic pathways. Role of auxin in determining pathogenesis in susceptible and resistant lines were imperative. The qPCR expression study of four LRR-RLK (Leucine-rich repeat receptor-like protein kinases) genes showed higher expression at 24 hrs after inoculation with pathogen. In summary, the conceptual model of induced resistance in wheat contributes insights on defense responses and imparts knowledge of Puccinia triticina-induced defense transcripts in wheat plants.
etinal image registration under the assumption of a spherical eye arlos

We propose a method for registering a pair of retinal images. The proposed approach employs point correspondences and assumes that the human eye has a spherical shape. The image registration problem is formulated as a 3D pose estimation problem, solved by estimating the rigid transformation that relates the views from which the two images were acquired. Given this estimate, each image can be warped upon
Utilisation of Bethesda system for reporting thyroid cytopathology: A study of 250 cases

Background: FNAC is a useful tool for initial diagnostic work up of thyroid nodule prior to both ultrasound and scintigraphy due to its diagnostic usefulness and cost-effectiveness. It is also useful if a suspicion of cancer exists. It has reduced the need of imaging and surgery and has increased the yield of cancer in patients who come for surgery. Terminology of reporting thyroid FNACs varied markedly from two category schemes to six or more category schemes making it difficult for clinicians to interpret the reports and hindered the sharing of clinically meaningful data among multiple institutions. To address this problem, the National Cancer Institute proposed a new system, named ‘the Bethesda system for reporting thyroid cytopathology’ (TBSRTC) in a conference organized in Bethesda. This system also described the risks of malignancy in each category and their recommended clinical management. Aim: To classify the thyroid lesions according to Bethesda system for reporting thyroid cytopathology and to find out the pathological spectrum of different thyroid lesions Material and methods: After taking approval from the institutional ethical committee and informed consent, this study was conducted on 250 cases at Department of Pathology SN Medical College, Jodhpur on patients aged between 10 to 70 years of any gender presenting with thyroid swelling. FNAC was performed and diagnosis given as per Bethesda classification. Results: Out of the total 250 cases studied 10 cases (4%) were Non Diagnostic/ Unsatisfactory, 220 cases (88%) were Benign, 5 cases (2%) were AUS, 4 cases (1.6%) were SFN/FN, 2 cases (0.8%) were Suspicious for malignancy and 9 cases (3.6%) were Malignant. Conclusion: TBSRTC provides uniform reporting system for thyroid FNA and as it has high specificity, it facilitates effective communication among health care providers.
Comparison between inter-rater reliability and inter-rater agreement in performance assessment.

INTRODUCTION Over the years, performance assessment (PA) has been widely employed in medical education, Objective Structured Clinical Examination (OSCE) being an excellent example. Typically, performance assessment involves multiple raters, and therefore, consistency among the scores provided by the auditors is a precondition to ensure the accuracy of the assessment. Inter-rater agreement and inter-rater reliability are two indices that are used to ensure such scoring consistency. This research primarily examined the relationship between inter-rater agreement and inter-rater reliability. MATERIALS AND METHODS This study used 3 sets of simulated data that was based on raters' evaluation of student performance to examine the relationship between inter-rater agreement and inter-rater reliability. RESULTS Data set 1 had high inter-rater agreement but low inter-rater reliability, data set 2 had high inter-rater reliability but low inter-rater agreement, and data set 3 had high inter-rater agreement and high inter-rater reliability. CONCLUSION Inter-rater agreement and inter-rater reliability can but do not necessarily coexist. The presence of one does not guarantee that of the other. Inter-rater agreement and inter-rater reliability are both important for PA. The former shows stability of scores a student receives from different raters, while the latter shows the consistence of scores across different students from different raters.
Viral Load Increases in SJL/J Mice Persistently Infected by Theiler's Virus after Inactivation of the β2m Gene

ABSTRACT We show that inactivating the β 2 m gene increases the viral load of SJL/J mice persistently infected by Theiler's virus. Together with previous results, this shows that the characteristics ofTmevp1, a locus which controls the amount of viral RNA that persists in the central nervous system, are those of an H-2class I gene.
5μW-to-10mW input power range inductive boost converter for indoor photovoltaic energy harvesting with integrated maximum power point tracking algorithm

Energy harvesting provides a means to supply wireless sensor networks in building environments with autonomous and sustainable power [1,2]. Indoor light can be converted into electricity by a solar cell and stored in a rechargeable battery or super-capacitor [3]. Depending on the indoor illumination level and the installed location as well as the orientation of the solar cell, the output power of an amorphous silicon solar cell can vary from less than a few μW/cm² up to hundreds of μW/cm² [3]. To manage the variation in both the illumination and panel size, a power-management circuit that is able to efficiently handle a wide range of input power is necessary. A solar cell can be modeled as a light-controlled current source in parallel with a diode. Its output current is determined by the output voltage in an exponential relation. At one point, the solar cell reaches its maximum power point (MPP). This MPP can be tracked by tuning either the output voltage or the load impedance [4].
Fast optimal energy-efficient resource allocation for downlink multi-user OFDM systems

In this paper, we propose an optimal resource allocation algorithm that maximizes the energy efficiency (EE) of a downlink (DL) multi-user orthogonal frequency division multiplexing (OFDM) system subject to a constraint on the total transmit power of the base station (BS). We show that the optimal EE is obtained by first allocating each subcarrier to the user equipment (UE) with the best channel power gain and then adapting the transmit power for each subcarrier using water-filling (WF) policy. Moreover, we propose a fast algorithm with linear complexity to compute the optimal WF level. We perform simulations to illustrate the effectiveness of the proposed algorithm and investigate the impact of maximum transmit power on the optimal EE. Simulation results indicate that an energy-efficient system behaves like a spectral-efficient system when the maximum transmit power of the BS is set to lower values.
Syngeneic transfer of autoimmune diabetes from diabetic NOD mice to healthy neonates. Requirement for both L3T4+ and Lyt-2+ T cells

We have developed a model of syngeneic adoptive transfer for type I diabetes mellitus of NOD mice. This model consists in injecting spleen cells from diabetic adult mice into newborn NOD recipients. 50% of recipients inoculated with 20 X 10(6) cells develop diabetes within the first 10 wk of life, at a time when none of the control littermates have yet become diabetic. The earliest successful transfers are observed at 3 wk of age, at a time when controls do not even exhibit histological changes in their pancreas. In addition we have shown that: (a) both males and females can be adoptively transferred, despite the fact that males rarely develop spontaneous diabetes in our colony; (b) diabetes transfer is a dose-dependent phenomenon that provides an in vivo assay for comparing the autoimmune potential of spleen cells from mice at various stages of their natural history; (c) the susceptibility of the recipients to the transfer is limited in time and declines after 3 wk; and (d) both L3T4+ and Lyt-2+ T cell subsets are necessary for the successful transfer. The neonatal syngeneic transfer provides an effective model for studies of the cellular events involved at regulatory and effector stages of autoimmune type I diabetes.
Consumer Referrals

In many industries, firms reward their customers for making referrals. We analyze the optimal policy mix of price, advertising intensity, and referral fee for a monopoly when buyers choose to what extent to refer other consumers to the firm. We find that the firm uses its referral fee, but not its price or advertising level, to manage referrals. When consumers hold correct expectations about the true quality of the product, the firm charges the standard monopoly price. The firm always advertises less when it uses referrals. We extend the analysis to the case where consumer referrals can be targeted.
Novel agents in development for pediatric sarcomas

Purpose of review The survival curves for many pediatric sarcomas have remained flat for the past 2 decades or more and novel therapeutics – those small molecule medicines that selectively inhibit specific signaling molecules – have been slow to enter into pediatric practice. The preclinical basis for their use is reviewed here. Recent findings Preclinical and phase I studies showing efficacy of antiinsulin-like growth factor receptor 1 therapies for Ewing sarcoma have led to numerous ongoing clinical trials using these agents for Ewing and other sarcomas. Early studies of ERBB signaling as a target in sarcoma therapy have been tantalizing, but progress in this area has been controversial. In-vitro analysis of Src inhibitors suggested that these agents would prevent metastasis in osteosarcoma, whereas in-vivo analysis showed no effect on metastasis, underscoring the need for thorough preclinical investigations of promising new therapies to guide future clinical trials. Antiangiogenic and immunomodulatory therapies are gaining momentum in the pediatric arena and should be tested in combination with traditional cytotoxic agents for recurrent and high-risk primary pediatric sarcomas. Summary Pediatric sarcomas have diverse biology and distinct signaling pathways, making detailed preclinical evaluation of small molecule inhibitors essential to guiding the design of further clinical investigations.
Mutually exclusive mutations in NOTCH1 and PIK3CA associated with clinical prognosis and chemotherapy responses of esophageal squamous cell carcinoma in China

Background Recurrent genetic abnormalities that correlate with clinical features could be used to determine patients' prognosis, select treatments and predict responses to therapy. Esophageal squamous cell carcinoma (ESCC) contains genomic alterations of undefined clinical significance. We aimed to identify mutually exclusive mutations that are frequently detected in ESCCs and characterized their associations with clinical variables. Methods We analyzed next-generation-sequencing data from 104 ESCCs from Taihang Mountain region of China; 96 pairs were selected for deep target-capture-based validation and analysis of clinical and pathology data. We used model proposed by Szczurek to identify exclusive mutations and to associate these with pathology findings. Univariate and multivariate analyses with Cox proportional hazards model were used to examine the association between mutations and overall survival and response to chemotherapy. Findings were validated in an analysis of samples from 89 patients with ESCC from Taihang Mountain. Results We identified statistically significant mutual exclusivity between mutations in NOTCH1 and PIK3CA in ESCC samples. Mutations in NOTCH1 were associated with well-differentiated, early-stage malignancy and less metastasis to regional lymph nodes. Nonetheless, patients with NOTCH1 mutations had shorter survival times than patients without NOTCH1 mutations, and failed to respond to chemotherapy. In contrast, patients with mutations in PIK3CA had better responses to chemotherapy and longer survival times than patients without PIK3CA mutations. Conclusions In a genetic analysis of ESCCs from patients in China, we identified mutually exclusive mutations in NOTCH1 and PIK3CA. These findings might increase our understanding of ESCC development and be used as prognostic factors.
Exploring the Experience of Benefit Finding in Parents of Children with Cancer: A Grounded Theory Study

EXPLORING THE EXPERIENCE OF BENEFIT FINDING IN PARENTS OF CHILDREN WITH CANCER: A GROUNDED THEORY STUDY By Carol E. Zogran, Ph.D., R.N. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2008 Director: Rita H. Pickler, Ph.D., R.N. , Professor and Chair, Department of Family and Community Health Nursing The diagnosis of cancer in a child is one of the most significant stressors a parent can experience, and research in the area of stress-related effects of illness on parents has emerged in many areas. The majority of studies have focused on the potential or actual negative impact on parents during and after treatment of their child’s illness. However, studies that initially set out to explore the difficulties associated with coping with childhood cancer found that parents often reported positive aspects about the experience. There is now increasing interest and support for the study of “positive-health” factors that contribute to protective variables influencing the health and well being of parents, such as benefit finding. The present study aimed to illuminate the process of benefit finding in x parents of children with cancer and to develop a theoretical model of this process based on the findings. This grounded theory study resulted in a conceptual model that organized and depicted the constructs and structures related to the process of benefit finding. Through constant comparative analysis, the Basic Psychosocial Problem was identified as being overwhelmed with fear. The parents identified intervening conditions that helped move them from feeling overwhelmed to feeling that they could manage the fear. Many parents identified a specific event, an “epiphenomenon” that created a turning point for them. This event, along with the intervening conditions, moved the parent from being overwhelmed to managing/transforming the fear, which was the Basic Psychosocial Process. The strategies that the parents identified as helping to manage the fear are being in the present, being strong, having faith/maintaining hope, and making meaning out of the event, of which benefit finding was the major component. This entire process occurred within the context of being a parent, as this awareness colored the entire experience. Benefit finding emerged as both a strategy and an outcome within this process and encompassed a growth in character, strengthening of relationships, and a gain in perspective. The theoretical model and substantive theory that emerged during the course of this study provide a way to understand this process in parents of children with cancer. CHAPTER
Successful therapy with anakinra in a patient with generalized pustular psoriasis carrying IL36RN mutations

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Design optimization of beam-like ferroelectrics-silicon microphone and microspeaker

Design optimization of beam-like ferroelectrics-silicon integrated microphone and microspeaker is studied. The Pt/Pb(Zr,Ti)O/sub 3//Pt/SiO/sub 2//Si/sub 3/N/sub 4/ cantilever structure is designed theoretically using multimorph model. The sensitivity and the sound pressure level (SPL) of the integrated microphone and microspeaker are calculated. It is found that the sensitivity of the microphone and the SPL of the microspeaker are very high. This integrated microphone and microspeaker will be valuable for high quality micro-acoustic devices.
Snapshots of protein folding. A study on the multiple transition state pathway of cytochrome c(551) from Pseudomonas aeruginosa.

Cytochrome c(551) (cyt c(551)) from Pseudomonas aeruginosa is a small protein (82 residues) that folds via a three-state pathway with the accumulation in the microsecond time-range of a compact collapsed intermediate. The presence of a single His residue, at position 16, permits the study of the refolding at pH 7.0 in the absence of miscoordination events. Here, we report on folding kinetics in the millisecond time-range as a function of urea under different pH conditions. Analysis of this process (over-and-above proline cis-trans isomerization) at pH 7.0, suggests the existence of a multiple transition state pathway in which we postulate three transition states. Taking advantage of site-directed mutagenesis we propose that the first "unfolded-like" transition state (t(1)) originates from the electrostatic properties of the collapsed state, while the second transition state (t(2)) involves the interaction between the N and C-terminal helices and is stabilized by the salt bridge between Lys10 and Glu70 ( approximately 1 kcal mol(-1)). Our results suggest that, contrary to other cytochromes c, the roll-over effect observed for cyt c(551) at low denaturant concentration can be interpreted in terms of a broad energy barrier without population of any intermediates. The third and more "native-like" transition state (M) can be associated with the breaking/formation of the Fe(3+)-Met61 bond. This strong interaction is stabilized by the hydrogen bond between Trp56 and heme propionate 17 (HP-17) as suggested by the increase in the unfolding rate at high denaturant concentration of the Trp56Phe site-directed mutant.
Conquering the Divide: Continuous Clustering of Distributed Data Streams

Data is often collected over a distributed network, but in many cases, is so voluminous that it is impractical and undesirable to collect it in a central location. Instead, we must perform distributed computations over the data, guaranteeing high quality answers even as new data arrives. In this paper, we formalize and study the problem of maintaining a clustering of such distributed data that is continuously evolving. In particular, our goal is to minimize the communication and computational cost, still providing guaranteed accuracy of the clustering. We focus on the k-center clustering, and provide a suite of algorithms that vary based on which centralized algorithm they derive from, and whether they maintain a single global clustering or many local clusterings that can be merged together. We show that these algorithms can be designed to give accuracy guarantees that are close to the best possible even in the centralized case. In our experiments, we see clear trends among these algorithms, showing that the choice of algorithm is crucial, and that we can achieve a clustering that is as good as the best centralized clustering, with only a small fraction of the communication required to collect all the data in a single location.