Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of a Reverse Transcription-PCR for Identification and Differentiation of Aichi Virus, a New Member of the Picornavirus Family Associated with Gastroenteritis in Humans

ABSTRACT Aichi viruses isolated in Vero cells from seven patients in five gastroenteritis outbreaks in Japan, five Japanese returning from Southeast Asian countries, and five local children in Pakistan with gastroenteritis were examined for differentiation based on their reactivities with a monoclonal antibody to a standard strain (A846/88) and a reverse transcription-PCR (RT-PCR) of three genomic regions. The RNA sequences were determined for 519 bases of these 17 isolates at the putative junction between the C terminus of 3C and the N terminus of 3D. The analyses revealed an approximately 90% homology between these isolates, which were then divided into two groups: group 1 (genotype A) included six isolates from four outbreaks and one isolate from a traveler and group 2 (genotype B) included one isolate from the other outbreak, four isolates from returning travelers, and all of the isolates from the Pakistani children. Based on the isolate sequences, a primer pair and a biotin-labeled probe were designed for amplification and detection of 223 bases at the 3C-3D junction of Aichi virus RNA in fecal specimens. The Aichi virus RNA was detected in 54 (55%) of 99 fecal specimens from the patients in 12 (32%) of 37 outbreaks of gastroenteritis in Japan. Of the 12 outbreaks, 11 were suspected to be due to genotype A. These results indicated that RT-PCR can be a useful tool to detect Aichi virus in stool samples and that a sequence analysis of PCR products can be employed to identify the prevalent strain in each incident.
Learning lost temporal fuzzy association rules

Fuzzy association rule mining discovers patterns in transactions, such as shopping baskets in a supermarket, or Web page accesses by a visitor to a Web site. Temporal patterns can be present in fuzzy association rules because the underlying process generating the data can be dynamic. However, existing solutions may not discover all interesting patterns because of a previously unrecognised problem that is revealed in this thesis. The contextual meaning of fuzzy association rules changes because of the dynamic feature of data. The static fuzzy representation and traditional search method are inadequate. The Genetic Iterative Temporal Fuzzy Association Rule Mining (GITFARM) framework solves the problem by utilising flexible fuzzy representations from a fuzzy rule-based system (FRBS). The combination of temporal, fuzzy and itemset space was simultaneously searched with a genetic algorithm (GA) to overcome the problem. The framework transforms the dataset to a graph for efficiently searching the dataset. A choice of model in fuzzy representation provides a trade-off in usage between an approximate and descriptive model. A method for verifying the solution to the hypothesised problem was presented. The proposed GA-based solution was compared with a traditional approach that uses an exhaustive search method. It was shown how the GA-based solution discovered rules that the traditional approach did not. This shows that simultaneously searching for rules and membership functions with a GA is a suitable solution for mining temporal fuzzy association rules. So, in practice, more knowledge can be discovered for making well-informed decisions that would otherwise be lost with a traditional approach.
Signaling pathways of replication stress in yeast

Eukaryotic cells activate the S-phase checkpoint in response to a variety of events affecting the progression of replication forks, collectively referred to as replication stress. This signaling pathway is divided in two branches: the DNA damage checkpoint (DDC) and the DNA replication checkpoint (DRC). Both pathways are activated by the sensor kinase Mec1 and converge on the effector kinase Rad53. However, the DDC operates throughout the cell cycle and depends on the checkpoint mediator Rad9 to activate Rad53, whereas the DRC is specific to S phase and is mediated by Mrc1 and other fork components to signal replication impediments. In this review, we summarize current knowledge on these two pathways, with a focus on the budding yeast Saccharomyces cerevisiae, in which many important aspects of the replication stress response were discovered. We also discuss the differences and similarities between DDC and DRC and speculate on how these pathways cooperate to ensure the complete and faithful duplication of the yeast genome under various replication stress conditions.
Challenges to Intervention Implementation: Lessons Learned in the Bathing Persons With Alzheimer's Disease at Home Study

Background: The pressing need for interventions to improve outcomes for vulnerable caregivers of individuals with Alzheimer's disease (AD) is hindered by inadequate knowledge of variables affecting intervention delivery, receipt, and enactment. Objective: To analyze intervention implementation issues encountered within the Bathing Persons with Alzheimer's Disease at Home (BATH) study. Methods: The BATH study, a home-based, randomized, controlled trial of interventions to improve behavioral symptoms and caregiver self-efficacy, consisted of 130 intervention visits to 42 care recipients-caregiver dyads. Data include direct observation, nurse interventionist field notes, case analyses, and caregiver journals, reflecting various perspectives. Content analysis was used to identify key treatment process themes. Results: Issues that affected the delivery, receipt, and enactment of interventions reflect the intersection of in vivo caregiving and research design. Discussion: The primary lessons learned were: (a) early identification of caring dyads prior to crisis must be improved; (b) in vivo observation is essential to individualized interventions targeting behavioral etiologies and developing caregiver skills; (c) intervention delivery depends on the nurse interventionist's skills and a flexible, trusting researcher-dyad relationship; (d) complex caregiver situations affect treatment receipt and enactment; and (e) intervention enactment requires coaching, practice, and support over time. These findings help to explain issues impacting intervention implementation to a vulnerable population. Recommendations for intervention research design to maximize internal and external validity in real-life care contexts can inform future outcome studies, aid in the search for improved care, and lead to supportive public policy for families living with AD.
Reducing Children's Risk for Later Reading Disabilities: The Role of Tier 1 and Tier 2 Instruction in Preschool.

The acquisition of reading and writing skills is a key developmental milestone as well as a significant educational achievement for children in a literate society. Reading and writing skills serve as the cornerstone to acquiring content knowledge in other domains both in school and throughout life. Moreover, as opportunities for employment have shifted toward technology and information-oriented jobs in the United States and elsewhere, well-developed literacy skills have become increasingly important. Despite the importance of literacy skills to educational and occupational opportunities and success, many children in the United States struggle with learning to read (e.g., see National Assessment of Educational Progress; National Center on Educational Statistics, 2007). Over the past two decades, there has been growing recognition of the significance of the preschool years for the development of later academic skills, including reading. Research has highlighted the importance of the preschool years for becoming a skilled reader, with a focus on what is called emergent literacy. Emergent literacy includes the skills, knowledge, and attitudes that are developmental precursors to conventional forms of reading and writing (Whitehurst & Lonigan, 1998). These emergent literacy skills are conceptualized as the basic building blocks onto which children’s later literacy skills are built. Because most preschool-age children are not yet reading or writing in conventional ways, instructional interventions during the preschool period most likely need to focus on helping children develop their emergent literacy skills. Children with well-developed emergent literacy skills are those children least likely to develop later reading problems. With the growing recognition of the potential contributions of the preschool period for children’s educational successes or difficulties, there has been increased attention to how instructional activities during preschool can help shape children’s educational outcomes--particularly for children at-risk of later reading difficulties. Some of this work can be informed by a “response to instruction” (RTI) approach that uses children’s acquisition of key skills in different instructional contexts to determine the likely future trajectory of children’s skills, the level of intensity of instruction needed to promote adequate learning, or both. In this paper, we discuss research findings that identify the skills most strongly related to the development of skilled reading and evidence of effectiveness for classroom-level and more individualized instructional strategies to promote the development of these skills. We also discuss the results of some of our recent studies that provide evidence for the effectiveness of some of these more individualized instructional activities in different classroom-level contexts. Finally, we discuss the implications of these findings for the application of the RTI approach in preschool settings to reduce the incidence of serious reading difficulties.
The canine parasternal and external intercostal muscles drive the ribs differently

1 In the dog, the elevation of the ribs during inspiration results from the combined actions of the parasternal and external intercostal muscles. In the present studies, the hypothesis was tested that co‐ordinated activity among these two sets of muscles reduces the distortion of the rib cage. 2 During spontaneous inspiration before or after section of the phrenic nerves, the ribs moved cranially and outward in the same way as they did during passive inflation. However, whereas the sternum moved cranially during passive inflation, it was displaced caudally during spontaneous inspiration. 3 When the parasternal intercostal muscles were selectively denervated, both the sternum and the ribs moved cranially, but the rib outward displacement was markedly reduced. In contrast, when the external intercostals were excised and the parasternal intercostals were left intact, the sternum continued to move caudally and the outward displacement of the ribs was augmented relative to their cranial displacement. 4 These observations establish that the external intercostal muscles drive the ribs primarily in the cranial direction, whereas the parasternal intercostals drive the ribs both cranially and outward. They also indicate, in agreement with the hypothesis, that co‐ordinated activity among these two sets of muscles displaces the ribs on their relaxation curve. 5 However, this co‐ordinated activity also displaces the sternum caudally. Although this distortion requires an additional energy expenditure, it enhances the outward component of rib displacement which is more effective with respect to lung expansion.
Connective tissue attachment to periodontally diseased roots after citric acid demineralization.

PREVIOUS INVESTIGATIONS have demonstrated that application of citric acid to a root surface results in exposure of dentin and/or cementum matrix collagen fibrils. Several studies have suggested a rapid and consistent connective tissue reattachment to citric acid treated roots. This study was initiated to determine if such an attachment was obtainable on human periodontally diseased teeth, in vivo, and could be confirmed through observations using the scanning electron and light microscopes. Full thickness flaps were raised on 18 single rooted teeth with moderate to advanced periodontitis. Citric acid (pH = 1.0) was applied to nine teeth with contralateral teeth serving as controls. Six to fifteen weeks later, the teeth with attached periodontal tissue were removed. Sagittal sections were obtained, with one-half of the root being processed for light microscopy and the remaining half studied by scanning electron microscopy. Six of nine citric acid treated roots provided evidence of fibrous attachment. Connective tissue was apposed directly to old or newly formed cementum, but never directly to dentin. Fibrous attachment was usually functionally oriented, i.e., perpendicular to the root surface. No evidence of fibrous attachment was found among the control specimens.
Endocrine aspects of female sexual dysfunction.

INTRODUCTION Various endogenous hormones, including estrogen, testosterone, progesterone and prolactin, may influence female sexual function. AIM To provide recommendations for the diagnosis and treatment of women with endocrinologic sexual difficulties. METHODS The Endocrine Aspects of Female Sexual Dysfunction Committee was part of a multidisciplinary International Consultation. It included four experts from two countries and several peer reviewers. MAIN OUTCOME MEASURE Expert opinion was based on committee discussion, a comprehensive literature review and evidence-based grading of available publications. RESULTS The impact of hormones on female sexual function and their etiological roles in dysfunction is complex. Research data are limited as studies have been hampered by lack of precise hormonal assays and validated measures of sexual function in women. Sex steroid insufficiency is associated with urogenital atrophy and may also adversely affect central sexual thought processes. Systemic estrogen/estrogen progestin therapy alleviates climacteric symptoms but there is no evidence that this therapy specifically improves hypoactive sexual desire disorder (HSDD) in premenopausal or postmenopausal women. Exogenous testosterone has been shown in small randomized controlled trials (RCT) to improve sexual desire, arousal and sexual satisfaction in both premenopausal and postmenopausal women. However, as there is no biochemical measure that clearly identifies who to treat, use of exogenous testosterone should be considered only after other causes of HSDD have been excluded, such as depression, relationship problems and ill health. The clinical assessment of HSDD should include detailed medical, gynecologic, sexual and psychosocial history and physical examination including the external/internal genitalia. Hormonal therapy should be individualized and risks/benefits fully discussed, and all treated women should be carefully followed up and monitored for therapeutic side effects. CONCLUSIONS There is a need for prospective, multi-institutional clinical trials to define safe and effective endocrine treatments for female sexual dysfunction.
Kabuki make-up (Niikawa-Kuroki) syndrome: a study of 62 patients.

These 62 patients with the Kabuki make-up syndrome (KMS) were collected in a collaborative study among 33 institutions and analyzed clinically, cytogenetically, and epidemiologically to delineate the phenotypic spectrum of KMS and to learn about its cause. Among various manifestations observed, most patients had the following five cardinal manifestations: 1) a peculiar face (100%) characterized by eversion of the lower lateral eyelid; arched eyebrows, with sparse or dispersed lateral one-third; a depressed nasal tip; and prominent ears; 2) skeletal anomalies (92%), including brachydactyly V and a deformed spinal column, with or without sagittal cleft vertebrae; 3) dermatoglyphic abnormalities (93%), including increased digital ulnar loop and hypothenar loop patterns, absence of the digital triradius c and/or d, and presence of fingertip pads; 4) mild to moderate mental retardation (92%); and 5) postnatal growth deficiency (83%). Thus the core of the phenotypic spectrum of KMS is rather narrow and clearly defined. Many other inconsistent anomalies were observed. Important among them were early breast development in infant girls (23%), and congenital heart defects (31%), such as a single ventricle with a common atrium, ventricular septal defect, atrial septal defect, tetralogy of Fallot, coarctation of aorta, patent ductus arteriosus, aneurysm of aorta, transposition of great vessels, and right bundle branch block. Of the 62 KMS patients, 58 were Japanese, an indication that the syndrome is fairly common in Japan. It was estimated that its prevalence in Japanese newborn infants is 1/32,000. All the KMS cases in this study were sporadic, the sex ratio was even, there was no correlation with birth order, the consanguinity rate among the parents was not high, and no incriminated agent was found that was taken by the mothers during early pregnancy. Three of the 62 patients had a Y chromosome abnormality involving a possible common breakpoint (Yp11.2). This could indicate another possibility, i.e., that the KMS gene is on Yp11.2 and that the disease is pseudoautosomal dominant. These findings are compatible with an autosomal dominant disorder in which every patient represents a fresh mutation. The mutation rate was calculated at 15.6 X 10(6).
Probabilistic defect occupancy model for NBTI

A new Negative Bias Temperature Instability (NBTI) model based on the probability of charge/discharge of defects in devices is presented. The model correctly describes the main experimental NBTI features, such as the threshold voltage shift (ΔVT) evolution under DC or AC stresses, its frequency and duty cycle dependence and the statistical ΔVT distribution in small transistors. Finally, the model is used to explain the dependence of NBTI degradation on the stress/relaxation times, frequency and duty cycle in terms of defect occupancy.
Upper abdominal cancer surgery in the very elderly

From January 1981 to December 1987, 59 major upper abdominal operations were performed on 57 patients aged 80 to 90 years at Memorial Sloan‐Kettering Cancer Center. Procedures for primary adenocarcinoma of the stomach, distal esophagus, pancreas, or hepatobiliary system were performed with curative intent or for palliation in 34 of 59 patients (58%) and bypass with limited or no resection in 13 of 59 patients (22%) patients. Emergency operations were performed in six (10%) patients for gastric bleeding, perforation, or outlet obstruction. Six (10%) patients underwent laparotomy for benign biliary obstruction (1), splenectomy for secondary thrombocytopenia (2), or gastrectomy for sarcoma (2) or lymphoma (1). Hospital mortality was 15% overall and 9% for major resections, 15% for bypass, and 67% for emergency procedures. Major complications occurred in 10 (20%) elective procedures. Mortality was associated with respiratory or cardiac failure while complications most commonly included arrhythmias and wound infection. Mean postoperative hospitalization was 18 days overall and 45 patients (76%) were discharged home. Median survival following major resection was 17.5 months but less than 2 months after bypass procedures. A protocol of pre‐operative evaluation, intra‐operative hemodynamic monitoring and postoperative intensive care has been formalized for use in elderly or poor‐risk patients.
Resveratrol modifies biliary secretion of cholephilic compounds in sham-operated and cholestatic rats

AIM To investigate the effect of resveratrol on biliary secretion of cholephilic compounds in healthy and bile duct-obstructed rats. METHODS Resveratrol (RSV) or saline were administered to rats by daily oral gavage for 28 d after sham operation or reversible bile duct obstruction (BDO). Bile was collected 24 h after the last gavage during an intravenous bolus dose of the Mdr1/Mrp2 substrate azithromycin. Bile acids, glutathione and azithromycin were measured in bile to quantify their level of biliary secretion. Liver expression of enzymes and transporters relevant for bile production and biliary secretion of major bile constituents and drugs were analyzed at the mRNA and protein levels using qRT-PCR and Western blot analysis, respectively. The TR-FRET PXR Competitive Binding Assay kit was used to determine the agonism of RSV at the pregnane X receptor. RESULTS RSV increased bile flow in sham-operated rats due to increased biliary secretion of bile acids (BA) and glutathione. This effect was accompanied by the induction of the hepatic rate-limiting transporters for bile acids and glutathione, Bsep and Mrp2, respectively. RSV also induced Cyp7a1, an enzyme that is crucial for bile acid synthesis; Mrp4, a transporter important for BA secretion from hepatocytes to blood; and Mdr1, the major apical transporter for xenobiotics. The findings were supported by increased biliary secretion of azithromycin. The TR-FRET PXR competitive binding assay confirmed RSV as a weak agonist of the human nuclear receptor PXR, which is a transcriptional regulator of Mdr1/Mrp2. RSV demonstrated significant hepatoprotective properties against BDO-induced cirrhosis. RSV also reduced bile flow in BDO rats without any corresponding change in the levels of the transporters and enzymes involved in RSV-mediated hepatoprotection. CONCLUSION Resveratrol administration for 28 d has a distinct effect on bile flow and biliary secretion of cholephilic compounds in healthy and bile duct-obstructed rats.
Optimal object grasp using tactile sensors and fuzzy logic

Optimal control of fingertip force during grasping operation by multifingered robotic end effectors is an important consideration. Determination of optimal fingertip force is, however, very complicated due to the involvement of a number of contact parameters at the finger-object interface including the mass of the object and the frictional properties of the contact surfaces. Modelling of various contact parameters is computationally overloading, which may not be tenable in practical situations where objects of different mass and material are available. Also for an unknown and unstructured environment, these properties may not be known in advance. This paper presents a controller based on fuzzy logic which is capable of performing optimal grasp of objects without knowing their mass and frictional properties. The controller also accounts for stability and dynamic aspects of the grasp. The experimental results of the implementation are presented.
Genetic variation and differentiation in parent-descendant cattle and bison populations 1 , 2 , 3

Genetic variation and differentiation at 32 microsatellite loci was quantified for parent-descendant cattle populations and parent-descendant bison (Bison bison) populations. We compared heterozygosity (Ho) and allelic richness (AR) for 587 cattle of four breeds and three lines derived from them, and 188 bison in three pairs of parent-descendant populations. Ho and AR were less in the Line 1 Hereford inbred cattle population than in the parent Hereford breed. Ho and AR were intermediate in a composite population (CGC, derived from crossing Red Angus, Charolais, and Tarentaise) compared to the three parent breeds. Crossbreeding of Line 1 with CGC resulted in an F1 generation with increased Ho and AR relative to Line 1 and CGC, followed by decreased Ho and AR in 2 backcross generations to Line1. Three transplanted wild bison populations had smaller Ho and AR than their respective parent populations. These data demonstrate that genetic variation reduced from founder effects or inbreeding can be restored with crossbreeding and gene flow.