Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic Analysis of Seed Coats in Yellow-Seeded Brassica napus Reveals Novel Genes That Influence Proanthocyanidin Biosynthesis

Yellow seeds are a favorable trait for Brassica crops breeding due to better quality than their black-seeded counterparts. Here, we compared the Brassica napus seed coat transcriptomes between yellow- and brown-seeded near-isogenic lines (Y-NIL and B-NIL) that were developed from the resynthesized yellow-seeded line No. 2127-17. A total of 4,974 differentially expressed genes (DEG) were identified during seed development, involving 3,128 up-regulated and 1,835 down-regulated genes in yellow seed coats. Phenylpropanoid and flavonoid biosynthesis pathways were enriched in down-regulated genes, whereas the top two pathways for up-regulated genes were plant–pathogen interaction and plant hormone signal transduction. Twelve biosynthetic genes and three regulatory genes involved in the flavonoid pathway exhibited similar expression patterns in seed coats during seed development, of which the down-regulation mainly contributed to the reduction of proanthocyanidins (PAs) in yellow seed coats, indicating that these genes associated with PA biosynthesis may be regulated by an unreported common regulator, possibly corresponding to the candidate for the dominant black-seeded gene D in the NILs. Three transcription factor (TF) genes, including one bHLH gene and two MYB-related genes that are located within the previous seed coat color quantitative trait locus (QTL) region on chromosome A09, also showed similar developmental expression patterns to the key PA biosynthetic genes and they might thus potentially involved participate in flavonoid biosynthesis regulation. Our study identified novel potential TFs involved in PAs accumulation and will provide pivotal information for identifying the candidate genes for seed coat color in B. napus.
An Economic Analysis of Color-Blind Affirmative Action

This article offers an economic analysis of color-blind alternatives to conventional affirmative action policies in higher education, focusing on efficiency issues. When the distribution of applicants' traits is fixed (i.e., in the short-run) color blindness leads colleges to shift weight from academic traits that predict performance to social traits that proxy for race. Using data on matriculates at several selective colleges and universities, we estimate that the short-run efficiency cost of "blind" relative to "sighted" affirmative action is comparable to the cost colleges would incur were they to ignore standardized test scores when deciding on admissions. We then build a model of applicant competition with endogenous effort in order to study long-run incentive effects. We show that, compared to the sighted alternative, color-blind affirmative action is inefficient because it flattens the function mapping effort into a probability of admission in the model's equilibrium. "Implementing race-neutral programs will help educational institutions minimize litigation risks they currently face… . If we are persistent in implementing race-neutral approaches, the end result will be to fulfill the great words of Dr. Martin Luther King Jr., who dreamed of the day that all children will be judged by the content of their character and not the color of their skin. "--US Department of Education. Race-Neutral Alternatives in Postsecondary Education: Innovative Approaches to Diversity , Washington, D.C.: U.S. Department of Education, Office of Civil Rights March 2003, pp. 7, 40. The Author 2007. Published by Oxford University Press on behalf of Yale University. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org, Oxford University Press.
NBER WORKING PAPER SERIES THE BEHAVIORALIST AS POLICY DESIGNER: THE NEED TO TEST MULTIPLE TREATMENTS TO MEET MULTIPLE TARGETS

We explore Tinbergen’s fundamental insight that policymakers need at least as many policy instruments as targets. We extend this idea using a large natural field experiment in water resource management. We use social comparisons and loss-framed messages to help achieve two goals of our partner utility: getting consumers to purchase drought-resistant plants and reducing water use. Our results show that seemingly related behavioral instruments can affect different household decisions. By themselves, social comparisons and loss framing have no significant impact on the number of rebate requests; when combined, however, they lead to a 36% increase in requests. Only loss framing leads to a significant increase in the purchase of drought-resistant plants, and only the social comparison reduces water consumption. These results highlight the importance of testing different combinations of instruments, particularly when policymakers have multiple goals and the relationship between instruments and goals is uncertain. Robert Hahn University of Oxford robert.hahn@smithschool.ox. ac.uk Robert D. Metcalfe University of Chicago Saieh Hall for Economics 5757 S. University Avenue Chicago IL, 60637 rdmetc@gmail.com David Novgorodsky University of Chicago Saieh Hall for Economics 1126 E. 59th St. Chicago IL, 60637 davidnov@uchicago.edu Michael K. Price Experimental Economics Center Andrew Young School of Policy Studies Georgia State University P.O. Box 3992 Atlanta, GA 30302-3992 and NBER mprice25@gsu.edu
The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication

Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. Several of the co-opted host factors bind to the viral RNA, which plays multiple roles, including mRNA function, as an assembly platform for the viral replicase (VRC), template for RNA synthesis, and encapsidation during infection. It is likely that remodeling of the viral RNAs and RNA-protein complexes during the switch from one step to another requires RNA helicases. In this paper, we have discovered a second group of cellular RNA helicases, including the eIF4AIII-like yeast Fal1p and the DDX5-like Dbp3p and the orthologous plant AtRH2 and AtRH5 DEAD box helicases, which are co-opted by tombusviruses. Unlike the previously characterized DDX3-like AtRH20/Ded1p helicases that bind to the 3′ terminal promoter region in the viral minus-strand (−)RNA, the other class of eIF4AIII-like RNA helicases bind to a different cis-acting element, namely the 5′ proximal RIII(−) replication enhancer (REN) element in the TBSV (−)RNA. We show that the binding of AtRH2 and AtRH5 helicases to the TBSV (−)RNA could unwind the dsRNA structure within the RIII(−) REN. This unique characteristic allows the eIF4AIII-like helicases to perform novel pro-viral functions involving the RIII(−) REN in stimulation of plus-strand (+)RNA synthesis. We also show that AtRH2 and AtRH5 helicases are components of the tombusvirus VRCs based on co-purification experiments. We propose that eIF4AIII-like helicases destabilize dsRNA replication intermediate within the RIII(−) REN that promotes bringing the 5′ and 3′ terminal (−)RNA sequences in close vicinity via long-range RNA-RNA base pairing. This newly formed RNA structure promoted by eIF4AIII helicase together with AtRH20 helicase might facilitate the recycling of the viral replicases for multiple rounds of (+)-strand synthesis, thus resulting in asymmetrical viral replication.
Joint Chance-Constrained Predictive Resource Allocation for Energy-Efficient Video Streaming

Predictive resource allocation (PRA) techniques that exploit knowledge of the future signal strength along roads have recently been recognized as promising approaches to save base station (BS) energy and improve user quality of service (QoS). Recent studies on human mobility patterns and wireless signal strength measurements along buses and trains have indeed supported the practical potential of PRA. An unresolved challenge, however, is modeling the uncertainty in the predictions, and developing real-time robust solutions that incorporate probabilistic QoS guarantees. This is of paramount importance in PRA due to the prediction time horizon that adds considerable complexity and increases the rate uncertainty in the problem. With these developments in mind, this paper addresses energy-efficient PRA applied to stored video streaming using chance constrained programming. The proposed solution incorporates: 1) uncertainty in predicted user rates; 2) a joint level of probabilistic constraint satisfaction over a time horizon; and 3) both optimal gradient-based and real-time guided heuristic solutions. Our framework fundamentally differs from previous PRA work in the literature where nonstochastic approaches with assumptions of perfect prediction were primarily used to demonstrate the potential energy savings and QoS gains. Numerical simulations based on a standard compliant long term evolution (LTE) system are provided to examine and compare the developed solution. Unlike existing energy-efficient PRA, the proposed framework achieves the desired QoS level under imperfect channel predictions. This robustness is attained without compromising the energy-efficiency compared to opportunistic schedulers, and thus supports PRA implementation in practice.
Time to Culture Positivity and Sputum Smear Microscopy during Tuberculosis Therapy

Sputum smear microscopy is widely used for tuberculosis diagnosis and treatment monitoring. We evaluated the correlation between smear microscopy and time to liquid culture positivity during early tuberculosis treatment. The study included patients with smear-positive pulmonary tuberculosis hospitalized at a tuberculosis reference centre in Germany between 01/2012 and 05/2013. Patient records were reviewed and clinical, radiological and microbiological data were analysed. Sputum samples were collected before treatment initiation and weekly thereafter. A number of 310 sputum samples from 30 patients were analysed. Time to liquid culture positivity inversely correlated with smear grade (Spearman's rho −0.439, p<0.001). There was a better correlation within the first two months vs. after two months of therapy (−0.519 vs. −0.416) with a trend to a more rapid increase in time to positivity between baseline and week 2 in patients who culture-converted within the first two months (5.9 days vs. 9.4 days, p = 0.3). In conclusion, the numbers of acid-fast bacilli in sputum smears of patients with pulmonary tuberculosis and time to culture positivity for M. tuberculosis cultures from sputum are correlated before and during tuberculosis treatment. A considerable proportion of patients with culture conversion after two months of therapy continued to have detectable acid-fast bacilli on sputum smears.
THE IMPACT OF TASK TYPE AND DIVERGENT THINKING ON READING PROFICIENCY

Recent trends in pedagogy have focused on more effective ways of teaching reading for the impact it has on general language proficiency. In the present study, we aimed to explore the influence of the cognitive style, convergent/divergent thinking, on reading comprehension performance through convergent versus divergent task types. For this purpose, 93 Iranian EFL students who were 18-26 and studied at the B.S. level at University of Social Welfare and Rehabilitation Sciences were selected. Being within the same range of reading performance, they were given the Torrance Divergent Thinking Test and were assigned to two groups so that there were roughly equal numbers of divergent and convergent thinkers in each. Next, the two groups took the Nelson’s reading comprehension test to ensure initial reading ability homogeneity. The experimental and the control groups then received treatment in the form of task-based instruction through either divergent or convergent tasks respectively over a period of one semester. To assess the reading comprehension gains of the participants at the end of the treatment, four types of reading multiple choice items, i.e. simple factual, referential, inferential, and multiple-response items, were used. The collected data were analyzed through Multivariate ANOVA, using SPSS software. Results indicated that the best results were achieved when divergent thinkers of the divergent task type group answer referential, and multiple-response items whereas the worst results were obtained when convergent thinkers in the convergent task group’s performance on multiple-response items was used as the criterion for reading assessment. Results also showed that a task-based course of instruction through convergent or divergent tasks causes the participants to have respectively lower or higher gains on the divergent thinking test.
Asymptotic behavior of the Weyl tensor in higher dimensions

We determine the leading order fall-off behaviour of the Weyl tensor in higher dimensional Einstein spacetimes (with and without a cosmological constant) as one approaches infinity along a congruence of null geodesics. The null congruence is assumed to "expand" in all directions near infinity (but it is otherwise generic), which includes in particular asymptotically flat spacetimes. In contrast to the well-known four-dimensional peeling property, the fall-off rate of various Weyl components depends substantially on the chosen boundary conditions, and is also influenced by the presence of a cosmological constant. The leading component is always algebraically special, but in various cases it can be of type N, III or II.
Ammonium Induces Aberrant Blastocyst Differentiation, Metabolism, pH Regulation, Gene Expression and Subsequently Alters Fetal Development in the Mouse

Abstract The presence of ammonium in the culture medium has significant detrimental effects on the regulation of embryo physiology and genetics. Ammonium levels build up linearly over time in the culture medium when media containing amino acids are incubated at 37°C. Ammonium in the culture media significantly reduces blastocyst cell number, decreases inner cell mass development, increases apoptosis, perturbs metabolism, impairs the ability of embryos to regulate intracellular pH, and alters the expression of the imprinted gene H19. In contrast, the rate of blastocyst development and blastocyst morphology appear to be normal. The transfer of blastocysts exposed to ammonium results in a significant reduction in the ability to establish a pregnancy. Furthermore, of those embryos that manage to implant, fetal growth is significantly impaired. Embryos exposed to 300 μM ammonium are retarded by 1.5 days developmentally at Day 15 of pregnancy. It is therefore essential that culture conditions for mammalian embryos are designed to minimize the buildup of ammonium to prevent abnormalities in embryo physiology, genetic regulation, pregnancy, and fetal development.
Occupation and bladder cancer in a hospital-based case–control study in Spain

Objectives: We investigated the association between occupation and bladder cancer in a hospital-based case–control study conducted in Spain. Methods: 1219 patients with transitional cell carcinoma of the urinary bladder and 1271 controls selected from 18 hospitals in Spain between June 1998 and September 2000 provided detailed information on life-time occupational history, smoking habits, medical history, and other factors. We used unconditional logistic regression to calculate odds ratios (OR) and 95% confidence intervals (CI) for each occupation and industry, adjusting for age, hospital region, smoking duration, and employment in a high-risk occupation for bladder cancer. Results: Statistically significant increased risks were observed among men employed as machine operators in the printing industry (OR 5.4; 95% CI 1.6 to 17.7), among men employed in the transportation equipment industry (OR 1.6; 95% CI 1.1 to 2.6) and among those who had worked for ⩾10 years in the electrical/gas/sanitary services (OR 3.9; 95% CI 1.5 to 10.4) and in hotels and other lodgings (OR 3.1; 95% CI 1.3 to 7.3). Men who worked as miscellaneous mechanics and repairers (OR 2.0; 95% CI 1.1 to 3.6) and as supervisors in production occupations (OR 2.1; 95% CI 1.2 to 3.6) also had excess risks for bladder cancer. Male farmers and those who worked in crop and livestock production had decreased risks for bladder cancer. We found no significant associations between occupation or industry and bladder cancer risk among women. Conclusions: We did not observe excess bladder cancer risk for many of the occupations identified as being a priori at high risk. Examination of more detailed job exposure information should help clarify these associations.
Developmental abnormalities of the gonad and abnormal sex hormone concentrations in juvenile alligators from contaminated and control lakes in Florida.

The reproductive development of alligators from a contaminated and a control lake in central Florida was examined. Lake Apopka is adjacent to an EPA Superfund site, listed due to an extensive spill of dicofol and DDT or its metabolites. These compounds can act as estrogens. Contaminants in the lake also have been derived from extensive agricultural activities around the lake that continue today and a sewage treatment facility associated with the city of Winter Garden, Florida. We examined the hypothesis that an estrogenic contaminant has caused the current failure in recruitment of alligators on Lake Apopka. Supporting data include the following: At 6 months of age, female alligators from Lake Apopka had plasma estradiol-17 beta concentrations almost two times greater than normal females from the control lake, Lake Woodruff. The Apopka females exhibited abnormal ovarian morphology with large numbers of polyovular follicles and polynuclear oocytes. Male juvenile alligators had significantly depressed plasma testosterone concentrations comparable to levels observed in normal Lake Woodruff females but more than three times lower than normal Lake Woodruff males. Additionally, males from Lake Apopka had poorly organized testes and abnormally small phalli. The differences between lakes and sexes in plasma hormone concentrations of juvenile alligators remain even after stimulation with luteinizing hormone. Our data suggest that the gonads of juveniles from Lake Apopka have been permanently modified in ovo, so that normal steroidogenesis is not possible, and thus normal sexual maturation is unlikely. Imagesp680-aFigure 1.Figure 2.Figure 3. AFigure 3. BFigure 3. CFigure 4. AFigure 4. BFigure 4. CFigure 4. DFigure 5. AFigure 5. BFigure 5. C
Changes in morbidity after pancreatic resection: toward the end of completion pancreatectomy.

HYPOTHESIS Advances in specialized centers for pancreatic diseases have improved surgical morbidity and outcome. In the past, postoperative local complications (pancreatic fistulae) were causing most of the mortality. Now, more patients experience postoperative complications related to their comorbidity. DESIGN To report a prospective audit of a single center's experience with pancreatic resection during an 8-year period. SETTING Tertiary referral center focused on pancreatic diseases. PATIENTS AND INTERVENTIONS Six hundred seventeen consecutive patients underwent pancreatectomy between November 1, 1993, and August 31, 2001. The series included 468 pancreatic head resections (76%), 25 total pancreatectomies (4%), 88 left-sided resections (14%), and 36 others (6%). MAIN OUTCOME MEASURES Morbidity after pancreatic resection. RESULTS Postoperative in-hospital mortality was 1.6%, and the additional operation rate was 4.1%. Four patients died of surgical complications and 6 of systemic complications. Systemic morbidity was 18% and consisted primarily of cardiopulmonary complications (13%). The most frequent postoperative complication was delayed gastric emptying (14%), which caused significant prolongation of the hospital stay. No patients died of a postoperative pancreatic fistula, which occurred in 3.2%, and no completion pancreatectomies were necessary. CONCLUSIONS Pancreatic resections can be performed with considerable safety and a low rate of pancreatic complications. More patients die of systemic complications than in the past, which increases the demand for precise preoperative patient selection. Completion pancreatectomy should no longer be considered in patients with a pancreatic fistula.
Effect of a new physiotherapy concept on bone mineral density, muscle force and gross motor function in children with bilateral cerebral palsy.

OBJECTIVE The purpose of this study was to determine the effect of a new physiotherapy concept on bone density, muscle force and motor function in bilateral spastic cerebral palsy children. METHODS In a retrospective data analysis 78 children were analysed. The concept included whole body vibration, physiotherapy, resistance training and treadmill training. The concept is structured in two in-patient stays and two periods of three months home-based vibration training. Outcome measures were dual-energy x-ray absorption (DXA), Leonardo Tilt Table and a modified Gross Motor Function Measure before and after six months of training. RESULTS Percent changes were highly significant for bone mineral density, -content, muscle mass and significant for angle of verticalisation, muscle force and modified Gross Motor Function Measure after six months training. CONCLUSIONS The new physiotherapy concept had a significant effect on bone mineral density, muscle force and gross motor function in bilateral spastic cerebral palsy children. This implicates an amelioration in all International Classification of Functioning, Disability and Health levels. The study serves as a basis for future research on evidence based paediatric physiotherapy taking into account developmental implications.
The use of nasal dilator strips as a placebo for trials evaluating continuous positive airway pressure

OBJECTIVES: The aim of the current study was to compare the objective and subjective effects of continuous positive airway pressure to the use of nasal dilator strips in patients with acromegaly and moderate to severe obstructive sleep apnea. METHODS: We studied 12 patients with acromegaly and moderate to severe obstructive sleep apnea (male/females = 8/4, age = 52±8 ys, body mass index = 33.5±4.6 Kg/m2, apnea–hypopnea index = 38±14 events/h) who had been included in a randomized, crossover study to receive three months of treatment with continuous positive airway pressure and nasal dilator strips. All patients were evaluated at study entry and at the end of each treatment by polysomnography, and Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index and treatment satisfaction questionnaires. ClinicalTrials.gov: NCT01265121 RESULTS: The apnea–hypopnea index values decreased significantly with continuous positive airway pressure treatment but did not change with the use of nasal dilator strips. All of the subjective symptoms improved with both treatments, but these improvements were significantly greater with continuous positive airway pressure than with the nasal dilator strips. CONCLUSION: The use of nasal dilator strips had a much smaller effect on the severity of obstructive sleep apnea in patients with acromegaly and moderate to severe obstructive sleep apnea in comparison to the use of continuous positive airway pressure. Moreover, the improvement in several subjective parameters without any significant objective improvement in obstructive sleep apnea resulting from the use of nasal dilator strips is compatible with a placebo effect.