Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

Gene expression is a complex trait determined by various genetic and nongenetic factors. Among the genetic factors, allelic difference may play a critical role in gene regulation. In this study we globally dissected cis (allelic) and trans sources of genetic variation in F1 hybrids between two Arabidopsis thaliana wild accessions, Columbia (Col) and Vancouver (Van), using a new high-density SNP-tiling array. This array tiles the whole genome with 35-bp resolution and interrogates 250,000 SNPs identified from resequencing of 20 diverse A. thaliana strains. Quantitative assessment of 12,311 genes identified 3811 genes differentially expressed between parents, 1665 genes with allele-specific expression, and 1688 genes controlled by composite trans-regulatory variation. Loci with cis- or trans-regulatory variation were mapped onto sequence polymorphisms, epigenetic modifications, and transcriptional specificity. Genes regulated in cis tend to be located in polymorphic chromosomal regions, are preferentially associated with repressive epigenetic marks, and exhibit high tissue expression specificity. Genes that vary due to trans regulation reside in relatively conserved chromosome regions, show activating epigenetic marks and generally constitutive gene expression. Our findings demonstrate a method of global functional characterization of allele-specific expression and highlight that chromatin structure is intertwined with evolution of cis- and trans-regulatory variation.
Prospective monitoring of health problems among recreational runners preparing for a half marathon

Objectives While the health benefits of running are legitimately advocated, participation in running can also lead to health problems. There is a high range of reported prevalence rates especially of running-related overuse injuries in high-level athletes and during competition. Little consensus exists for acute injuries and illnesses especially in recreational runners. Therefore, the aim of this study was to record the prevalence of health problems in recreational long-distance runners preparing for an event. Methods Recreational runners aged 18–65 years who were registered 13 weeks prior to a half-marathon running event were invited to take part in this study. Participants were prospectively monitored weekly over 13 weeks by applying a standardised surveillance system for injuries and illnesses (Oslo Sports Trauma Research Center questionnaire). From this, prevalence and severity of acute and overuse injuries, as well as illnesses, were calculated. Results We received 3213 fully answered questionnaires from 327 participants (40.7% female, 40.9±11.7 years of age, 31.5±21.1 km weekly mileage, 8.3±7.8 years of running experience). At any point in time over the preparation phase, 37.3% of the participants had health problems. Overuse injuries were the major burden (18%). They were followed by illnesses (14.1%) and acute injuries (7.9%). The median weekly severity score was 56.5 (IQR 37.0–58.0). Conclusion The high prevalence of health problems in our cohort suggests that future efforts are needed to further specify the underlying mechanism and develop adequate prevention strategies for recreational runners.
Accelerated enhanced Recovery following Minimally Invasive colorectal cancer surgery (RecoverMI): a study protocol for a novel randomised controlled trial

Introduction Definitive treatment of localised colorectal cancer involves surgical resection of the primary tumour. Short-stay colectomies (eg, 23-hours) would have important implications for optimising the efficiency of inpatient care with reduced resource utilisation while improving the overall recovery experience with earlier return to normalcy. It could permit surgical treatment of colorectal cancer in a wider variety of settings, including hospital-based ambulatory surgery environments. While a few studies have shown that discharge within the first 24 hours after minimally invasive colectomy is possible, the safety, feasibility and patient acceptability of a protocol for short-stay colectomy for colorectal cancer have not previously been evaluated in a prospective randomised study. Moreover, given the potential for some patients to experience a delay in recovery of bowel function after colectomy, close outpatient monitoring may be necessary to ensure safe implementation. Methods and analysis In order to address this gap, we propose a prospective randomised trial of accelerated enhanced Recovery following Minimally Invasive colorectal cancer surgery (RecoverMI) that leverages the combination of minimally invasive surgery with enhanced recovery protocols and early coordinated outpatient remote televideo conferencing technology (TeleRecovery) to improve postoperative patien-provider communication, enhance postoperative treatment navigation and optimise postdischarge care. We hypothesise that RecoverMI can be safely incorporated into multidisciplinary practice to improve patient outcomes and reduce the overall 30-day duration of hospitalisation while preserving the quality of the patient experience. Ethics and dissemination RecoverMI has received institutional review board approval and funding from the American Society of Colorectal Surgeons (ASCRS; LPG103). Results from RecoverMI will be published in a peer-reviewed publication and be used to inform a multisite trial. Trial registration number NCT02613728; Pre-results.
Elaboration, Diversification and Regulation of the Sir1 Family of Silencing Proteins in Saccharomyces

Heterochromatin renders domains of chromosomes transcriptionally silent and, due to clonal variation in its formation, can generate heritably distinct populations of genetically identical cells. Saccharomyces cerevisiae's Sir1 functions primarily in the establishment, but not the maintenance, of heterochromatic silencing at the HMR and HML loci. In several Saccharomyces species, we discovered multiple paralogs of Sir1, called Kos1–Kos4 (Kin of Sir1). The Kos and Sir1 proteins contributed partially overlapping functions to silencing of both cryptic mating loci in S. bayanus. Mutants of these paralogs reduced silencing at HML more than at HMR. Most genes of the SIR1 family were located near telomeres, and at least one paralog was regulated by telomere position effect. In S. cerevisiae, Sir1 is recruited to the silencers at HML and HMR via its ORC interacting region (OIR), which binds the bromo adjacent homology (BAH) domain of Orc1. Zygosaccharomyces rouxii, which diverged from Saccharomyces after the appearance of the silent mating cassettes, but before the whole-genome duplication, contained an ortholog of Kos3 that was apparently the archetypal member of the family, with only one OIR. In contrast, a duplication of this domain was present in all orthologs of Sir1, Kos1, Kos2, and Kos4. We propose that the functional specialization of Sir3, itself a paralog of Orc1, as a silencing protein was facilitated by the tandem duplication of the OIR domain in the Sir1 family, allowing distinct Sir1–Sir3 and Sir1–Orc1 interactions through OIR–BAH domain interactions.
[Analysis of intrauterine sounds and their tranquillizing effects on the newborn infant].

The authors have made a piezo-electric microphone in order to tap and analyse intrauterine sounds. The band that is used ranges from 3 - 700 Hz. A sound that has a small microphone at its tip is introduced into the uterus and then relayed to an amplifier. The sound mainly comes from the blood vessels and their frequency ranges between a few Hz and a thous and Hz. The acoustic pressure is big for low frequencies and weak for high frequencies. The sounds that are heard in the uterus have a calming effect on new-born children and stop them crying in 86% of cases where it has been tried. It sends them to sleep in 30% and this has been confirmed by E.E.G. This method is more effective than the older ones which used "slumber tone". The reason is that the product is the same as that which has been experienced by the fetus in utero.
The Economics of Housing

Housing is an important commodity in the national accounts of all countries and has generated a high quality specialised literature. The papers in this scholarly collection span a thirty-five year period from 1960 when the field of housing economics was just beginning to attract attention. Topics covered include housing and urban spatial structures, housing supply, the analysis of housing demand and empirical and theoretical studies of housing quality and prices.
The Influence Study of Transformational Leadership in University on Teacher's Organizational Commitment: The Construction and Verification of a Theoretical Model

There is close relationship between teacher’s organizational commitment in university and educational quality. How did the leadership in university take effect on teacher’s organizational commitment? It is an urgent problem to explore and solve. This paper proposes a theoretical analytical model including transformational leadership, goal setting, self-efficacy, goal self-concordance and organizational commitment on the basis of discussing the function and relationship of mediating factor about self-efficacy, goal setting and goal self-concordance between transformational leadership in university and teacher’s organizational commitment. Using the sample of 309 data in China and Structural Equation Model, the present research empirically tests the direct and indirect effect of transformational leadership. The research changes our views on the role of goal setting, self-efficacy and goal self-concordance in the function mechanism of transformational leadership. At the same time, the results provide some references for leaders of universities on how to perfect the effectiveness of leadership by improving teachers’ autonomous motivation and organizational commitment.
Fabric Defect Detection for Apparel Industry: A Nonlocal Sparse Representation Approach

With the increasing customer demand on fabric variety in fashion markets, fabric texture becomes much more diverse, which brings great challenges to accurate fabric defect detection. In this paper, a fabric inspection model, consisting of image preprocessing, image restoration, and thresholding operation, is developed to address the woven fabric defect detection problem in the apparel industry, especially for fabric with complex texture and tiny defects. The image preprocessing first improves the image contrast in order to make the details of defects more salient. Based on the learned sub-dictionaries, a non-locally centralized sparse representation model is adopted to estimate the non-defective version of the input images, so that the possible defects can be easily segmented from the residual images of the estimated images and the inputs by thresholding operation. The performance of the proposed defect detection model was evaluated through extensive experiments with various types of real fabric samples. The proposed detection model was proved to be effective and robust, and superior to some representative detection models in terms of the detection accuracy and false alarms.
Nature, Nurture, and the Case for Nutrition Bacteria in the Gut: Friends and Foes and How to Alter the Balance 1

The activities of the bacteria resident in the colon of companion animals can have an impact upon the health of the host. Our understanding of this microbial ecosystem is presently increasing due to the development of DNA-based microbiological tools that allow identiﬁcation and enumeration of nonculturable microorganisms. These techniques are changing our view of the bacteria that live in the gut, and they are facilitating dietary-intervention approaches to modulate the colonic ecosystem. This is generally achieved by the feeding of either live bacteria (probiotics) or nondigestible oligosaccharides (prebiotics) that selectively feed the indigenous probiotics. Feeding studies with a Lactobacillus acidophilus probiotic have shown positive effects on carriage of Clostridium spp. in canines and on recovery from Campylobacter spp. infection in felines. Immune function was improved in both species. Prebiotic feeding studies with lactosucrose and fructo-oligosaccharides in both cats and dogs have shown positive effects on the microﬂora balance. Recently synbiotic forms (a probiotic together with a prebiotic) targeted at canines have been developed that show promise as dietary-intervention tools. J. Nutr. 134: 2022S–2026S, 2004.
Training Virtual Reality and Augmented Reality Prototyping without Coding

Recently, virtual reality (VR) and augmented reality (AR) applications have become popular. Hence, designers must be trained to be better equipped to design VR applications and games. However, current VR prototyping approaches present many obstacles to design students; for example, most applications require programming skills that involve a steep learning curve for design students without technical backgrounds. A VR/AR prototyping method that involves a gentle learning curve is thus required. This study proposed such a method, and conducted a 3-hour workshop with master-level design students. The outcome is reported in this paper. Observations and reflections are presented.
Overconfidence in a Career-Concerns Setting

We study the effects of overconfidence in a two-period investment-decision agency setting. Under common priors, agent risk aversion implies inefficiently low first-period investment. In our model, principal and agent disagree about the profitability of the investment decision conditional on a given public signal. An overconfident agent believes that the principal will update her beliefs upwards more often than not. As a consequence, the agent overestimates the benefits of learning from first-period investment. This implies that agent overconfidence mitigates the agency problems arising from the agent’s career concerns, even though an overconfident agent bears more project and reputational risk in equilibrium.
Clinical outcome of mitral regurgitation due to flail leaflet.

BACKGROUND Mitral regurgitation due to flail leaflet is difficult to manage, because it is frequently asymptomatic yet carries a high risk of left ventricular dysfunction and because the natural history of the condition is poorly defined. METHODS We obtained clinical follow-up data through 1994-1995 in 229 patients with isolated mitral regurgitation due to flail leaflet; this condition was first diagnosed by echocardiography between 1980 and 1989. RESULTS The 86 patients who were treated medically had a mortality rate significantly higher than expected (6.3 percent yearly, P=0.016 for the comparison with the expected rate in the U.S. population according to the 1990 census). Independent determinants of mortality were an older age, the presence of symptoms, and a lower ejection fraction. Patients who were even transiently in New York Heart Association functional class III or IV had a high mortality rate (34 percent yearly), but the rate was also notable (4.1 percent yearly) among those in class I or II. At 10 years, the mean (+/- SE) rates of heart failure, atrial fibrillation, and death or surgery were 63 +/- 8, 30 +/- 12, and 90 +/- 3 percent, respectively. In a multivariate analysis, surgical correction of mitral regurgitation (performed in 143 patients) was associated with a reduced mortality rate (hazard ratio, 0.29; 95 percent confidence interval, 0.15 to 0.56; P<0.001). CONCLUSIONS When treated medically, mitral regurgitation due to flail leaflet is associated with excess mortality and high morbidity. Surgery is almost unavoidable within 10 years after the diagnosis and appears to be associated with an improved prognosis; this finding suggests that surgery should be considered early in the course of the disease.
Dietary protein level affects protein metabolism during the postabsorptive state in dogs.

The effects of dietary protein level on whole-body protein metabolism have usually been assessed in dogs by nitrogen balance studies based on the difference between nitrogen intake and excretion from the body (1,2). Although this method has been widely accepted for evaluation of nutritional status and determination of dietary protein requirement (3), it fails to distinguish between the effects of individual changes in protein synthesis, oxidation and breakdown and the overall response of the body to altered nutritional intake. 13 C-Leucine infusion is now regarded as the reference method (4) for determination of whole-body protein metabolism. Theoreti-cally, the oxidation of any essential amino acid in steady-state conditions is accompanied by the catabolism of all amino acids in the proteins of origin and should thus provide information equivalent to that of total nitrogen excretion. In a previous study using 13 C-leucine infusion, our group estimated that the minimal nitrogen requirement in dogs is between 0.41 and 0.55 g N/kg metabolic body weight (BW 0.75 ) 4 per d (5). The kinetic parameters of protein metabolism in adult dogs can be modulated notably in the short term by food (energy) intake and in the long term by variations in whole-body protein which is also the case for However, very little is known about the effects of graded dietary protein level on whole-body protein kinetics in normally fed dogs. It is likely that modiﬁcations of whole-body protein kinetics occur once dogs adapt to graded dietary protein levels and that these changes are partly attributed to enhancement of the oxidative pathway by excess protein. In humans in the fasting state, graded dietary protein level has
Intravenous lipid emulsions in the critically ill: an update

Purpose of reviewPurpose of the review is to summarize recent research addressing the role of intravenous lipid emulsions (IVLEs) in the critically ill. Recent findingsSoybean oil-based IVLEs, which are high in the omega-6 polyunsaturated fatty acids, have been largely used in parenteral nutrition over the last several decades. However, it is now generally accepted that the higher content of phytosterols and polyunsaturated fatty acids in soybean oil IVLE may adversely affect the immunological and inflammatory status of the critically ill. In the last few years, alternative IVLEs with lower soybean oil content have been associated with important improvements in clinical outcomes, such as mortality, mechanical ventilation days, and ICU length of stay. Olive oil and fish oil IVLEs have been reported to reduce the incidence of infections, with no clear benefits in other clinical outcomes. Despite the promising results with these new parenteral nutrition strategies, the optimum composition, dosage and indication for alternative IVLEs still remain controversial. Nevertheless, according to current knowledge alternative IVLEs may be associated with improved clinical outcomes and should be considered in critically ill patients requiring parenteral nutrition. SummaryThere is a growing body of evidence suggesting that improved clinical outcomes can be achieved with selective use of alternative IVLEs in parenteral nutrition regimens for the critically ill. More high quality trials are needed, to better evaluate the efficacy of alternative IVLEs.
Decentralized localization in wireless sensor networks

Localization is an imperative stage in building a routing matrix between nodes in Wireless Sensors Network (WSN). It is essential for exchanging the measured Data in the network and making informed conclusions. This paper reviews the localization techniques for Wireless Sensor Networks Nodes. It presents a mathematical model for finding sensors locations based on Received Signal Strength Indicators (RSSI) and takes care of the measurement noise involved. It also carries out a comparison between centralized and decentralized localization in terms of the average consumed communication power by the network to achieve the localization of the nodes. Different scenarios are simulated by varying the geographical deployment area of the network and the number of nodes used. Evaluation results show that decentralized localization consumes less communication power and is more scalable than the centralized approach.
Prospective cohort study of soy food consumption and risk of bone fracture among postmenopausal women.

BACKGROUND Soy consumption has been shown to modulate bone turnover and increase bone mineral density in postmenopausal women. To our knowledge, no published studies have directly examined the association between soy consumption and risk of fracture. METHODS We examined the relationship between usual soy food consumption and fracture incidence in 24,403 postmenopausal women who had no history of fracture or cancer and were recruited between March 1, 1997, and May 23, 2000, in the Shanghai Women's Health Study, a cohort study of approximately 75,000 Chinese women aged 40 to 70 years. Usual soy food intake was assessed at baseline and reassessed during follow-up through in-person interviews using a validated food frequency questionnaire. Outcomes were ascertained by biennial in-person interview surveys. RESULTS During a mean follow-up of 4(1/2) years (110,243 person-years), 1770 incident fractures were identified. After adjustment for age, major risk factors of osteoporosis, socioeconomic status, and other dietary factors, the relative risks (95% confidence intervals) of fracture were 1.00, 0.72 (0.62-0.83), 0.69 (0.59-0.80), 0.64 (0.55-0.76), and 0.63 (0.53-0.76) across quintiles of soy protein intake (P<.001 for trend). The inverse association was more pronounced among women in early menopause. The multivariate relative risks (95% confidence intervals) of fracture comparing the extreme quintiles of soy protein intake were 0.52 (0.38-0.70) for women within 10 years of menopause vs 0.71 (0.56-0.89) for late postmenopausal women. Similar results were also found for intake of isoflavones. CONCLUSION Soy food consumption may reduce the risk of fracture in postmenopausal women, particularly among those in the early years following menopause.
Are Cementoblasts a Subpopulation of Osteoblasts or a Unique Phenotype?

Experimental studies have shown a great potential for periodontal regeneration. The limitations of periodontal regeneration largely depend on the regenerative potential at the root surface. Cellular intrinsic fiber cementum (CIFC), so-called bone-like tissue, may form instead of the desired acellular extrinsic fiber cementum (AEFC), and the interfacial tissue bonding may be weak. The periodontal ligament harbors progenitor cells that can differentiate into periodontal ligament fibroblasts, osteoblasts, and cementoblasts, but their precise location is unknown. It is also not known whether osteoblasts and cementoblasts arise from a common precursor cell line, or whether distinct precursor cell lines exist. Thus, there is limited knowledge about how cell diversity evolves in the space between the developing root and the alveolar bone. This review supports the hypothesis that AEFC is a unique tissue, while CIFC and bone share some similarities. Morphologically, functionally, and biochemically, however, CIFC is distinctly different from any bone type. There are several lines of evidence to propose that cementoblasts that produce both AEFC and CIFC are unique phenotypes that are unrelated to osteoblasts. Cementum attachment protein appears to be cementum-specific, and the expression of two proteoglycans, fibromodulin and lumican, appears to be stronger in CIFC than in bone. A theory is presented that may help explain how cell diversity evolves in the periodontal ligament. It proposes that Hertwig’s epithelial root sheath and cells derived from it play an essential role in the development and maintenance of the periodontium. The role of enamel matrix proteins in cementoblast and osteoblast differentiation and their potential use for tissue engineering are discussed.