Miracle-dz/UniFAR-FTUs huggingface dataset:
Rhizobium-Legume Symbiosis and Nitrogen Fixation under Severe Conditions and in an Arid Climate

SUMMARY Biological N2 fixation represents the major source of N input in agricultural soils including those in arid regions. The major N2-fixing systems are the symbiotic systems, which can play a significant role in improving the fertility and productivity of low-N soils. The Rhizobium-legume symbioses have received most attention and have been examined extensively. The behavior of some N2-fixing systems under severe environmental conditions such as salt stress, drought stress, acidity, alkalinity, nutrient deficiency, fertilizers, heavy metals, and pesticides is reviewed. These major stress factors suppress the growth and symbiotic characteristics of most rhizobia; however, several strains, distributed among various species of rhizobia, are tolerant to stress effects. Some strains of rhizobia form effective (N2-fixing) symbioses with their host legumes under salt, heat, and acid stresses, and can sometimes do so under the effect of heavy metals. Reclamation and improvement of the fertility of arid lands by application of organic (manure and sewage sludge) and inorganic (synthetic) fertilizers are expensive and can be a source of pollution. The Rhizobium-legume (herb or tree) symbiosis is suggested to be the ideal solution to the improvement of soil fertility and the rehabilitation of arid lands and is an important direction for future research.
Relationship between bone mineral density and dietary intake of β-carotene, vitamin C, zinc and vegetables in postmenopausal Korean women: a cross-sectional study

Objective To examine the relationship between nutritional intake and bone mineral density (BMD) in postmenopausal Korean women. Methods Dietary intake was recorded in postmenopausal Korean women using a semiquantitative questionnaire. The frequency of consumption of various food groups and nutrient intake were calculated. BMD T-scores were measured at the lumbar spine, femoral neck and total hip using dual-energy X-ray absorptiometry. Associations between T-scores and dietary intake were analysed using partial correlation coefficients and multiple linear regression analysis. Results A total of 189 postmenopausal women were included in the study. β-Carotene intake was positively correlated with the lumbar spine T-score. Sodium and vitamin C intake were positively associated and folate intake negatively associated with the femoral neck T-score. Sodium, zinc and vitamin C intake were positively correlated and potassium intake was negatively correlated with the total hip T-score. Vegetable intake showed a positive association with the femoral neck and total hip T-scores. Conclusion In postmenopausal Korean women, β-carotene, vitamin C, zinc and sodium intakes were positively associated with bone mass. Furthermore, frequency of vegetable consumption was positively associated with femoral neck and total hip T-scores.
Nature of Science: Past, Present, and Future

s International, 38, 5378A (University Microfilms No. 78-00, 998). Rubba, P. A. , & Andersen, H. (1978). Development of an instrument to assess secondary school students’ understanding of the nature of scientific knowledge. Science Education, 62(4), 449–458. Rubba, P., Horner, J., & Smith, J. M. (1981). A study of two misconceptions about the nature of science among junior high school students. School Science and Mathematics, 81, 221–226. Rudolph, J. L. (2003). Portraying epistemology: School science in historical context. Science Educa-
Validation of proteomic‐based discovery with tissue microarrays

Proteomics is routinely utilized for biomarker discovery above and beyond its general use in basic science. Multiple platforms provide a robust pipeline of candidates that require verification and validation as biomarkers of disease. Within the field of oncology, tissue biomarkers are in high demand as tools of diagnosis, prognosis and prediction of response to therapy. By examining the proteome, rather than the transcriptome, there is the potential to directly interrogate the drug targets and define biomarkers at the most proximate level. Toward these ends, the tissue microarray has become a common platform for verification of results and validation of clinically relevant biomarkers. Immunohistochemistry remains the most common analytical method applied to TMA and provides a direct channel toward clinical application. The TMA stands at the crossroads of proteomics and pathology, combining formalin‐fixed paraffin‐embedded tissue as an analyte and IHC as a method of assay.
Optimal Conditions for Polyclonal Antibody Secretion and DNA Synthesis in Human Blood and Spleen Lymphocytes by Lipopolysaccharide

Lipopolysaccliarides from E. coli (LPS) stimulated increased DNA synthesis and high‐rate antibody secretion in human lymphocytes from blood and spleen. Peak DNA synthesis by 10 or 100 μg/ml LPS was seen on day 6 for blood lymphocytes. Using 500 μg/ml of LPS the peak response was reached on day 5 and with 0.1–1 μg/ml the maximal stimulation was on day 7. For spleen cells LPS 100 μg/ml gave a peak stimulation on day 4 or 5. Antibody secretion, measured as plaque‐forming cells (PFC) against fluorescein isothiocyanate‐coupled sheep erythrocytes in a haemolysis‐in‐gel assay, was maximal on day 5 in blood lymphocytes and on day 3 or 4 in spleen cells. The highest cell viability and antibody secretion after stimulation with LPS was obtained in 16 mm diameter multiwell plates using 2.5 × 106 cells in 1 ml of medium containing 10% AB serum absorbed with SRBC. Feeding of cultures was essential for stimulation of blood lymphocytes but not for spleen cells.
Induction over Strategic Agents

We study the problem where a decision maker needs to discover a classification rule to classify intelligent, self-interested agents. Agents may engage in strategic behavior to alter their characteristics for a favorable classification. We show how the decision maker can induce a classification rule that anticipates such behavior while still satisfying an important risk minimization principle.
Efficacy of 2 Alcohol-Based Gels and 1 Alcohol-Based Rinse for Surgical Hand Disinfection

We assessed the efficacy of 2 alcohol-based gels and 1 alcohol-based rinse for surgical hand disinfection, using European standard EN 12791. Volunteers performed surgical hand disinfection with a reference product and each of the 3 study products, with 1-week intervals between disinfection episodes. The immediate and sustained antimicrobial activities of each study product were not significantly less than those of the reference product. The study products passed the efficacy requirements of the EN 12791 standard, and they are considered suitable for surgical hand disinfection.
Vaccination to prevent persistent viral infection

Persistent virus infections are increasingly being recognized as a significant cause of human morbidity and mortality. To establish persistence, a virus must establish infection and evade eradication by the host immune response, in particular by cytotoxic T lymphocytes (CTL). We have studied a virus that establishes persistence in part by suppressing the CTL response of the infected host. The virus persists in many cell types, including lymphocytes and macrophages. We show that prior immunization with a vaccine designed to induce CTL (in the absence of antiviral antibody) confers complete protection against subsequent establishment of persistence in all tissues analyzed. The vaccine can be designed to express as few as 10 amino acids of a viral protein that comprise the CTL epitope. Further, two CTL epitopes for two discrete MHC haplotypes can be successfully used in a single vaccine that protects both strains of mice. Hence, a "string of CTL epitopes" (beads) concept for vaccination is feasible. Finally, the CTL vaccine provided protection against the establishment of persistence by an immunosuppressive virus.
Anxious depression among Puerto Rican and African-American older adults

Objectives: To determine racial/ethnic differences in the prevalence and impact of anxious depression (i.e. major depressive disorder, MDD, occurring concomitant with generalized anxiety symptoms) among older adults. Method: Interviews were conducted with 218 Puerto Rican and 206 African American older (age ≥60) urban senior housing residents. Data were collected on diagnostic status, depression severity and psychosocial functioning. Results: Results indicated a higher prevalence of MDD and anxious depression among Puerto Rican participants. Anxious depression was associated with more severe ratings of distress and suicidality compared with MDD alone, and the impact of depression and anxiety was most pronounced for the Puerto Rican participants. Puerto Rican participants also reported poorer subjective health and more substantial disability; however, these effects were independent of depression or anxiety status. Conclusions: Anxious depression is common among older ethnic minority adults and the impact of these symptoms differs by race/ethnicity. These results highlight the importance of conducting culturally sensitive assessments of depression and anxiety among older adults.
Evaluation of three radiographic methods for detecting occlusal caries lesions

Aim: To compare, in vitro, the performance of three radiographic methods for the detection of occlusal caries in permanent teeth. Methods: A total of 96 extracted molars with no apparent occlusal cavitation were selected, they were photographed and radiographed under standardized conditions using conventional E-plus films and two digital systems, CDR and Sidexis. Two examiners analyzed all films and images, recording the presence and lesion depth. One quarter of the teeth were re-examined for intra- and interexaminer agreements. The teeth were subsequently bisected and examined under a stereomicroscope. The intra and interexaminer agreements and the diagnostic performance (sensitivity, specificity, accuracy and the area under receiver operating characteristic, ROC curve) of each method were evaluated. Results: Out of 96 occlusal surfaces, 41 were sound, 31 had lesions in enamel, and 24 had dentin lesions. Weighted Kappa values for intraexaminer agreement varied widely, depending on both the observer and method. The interexaminer agreement was higher for the digital images than for the conventional films. The area under the ROC curve for enamel and dentin caries (at D1 diagnostic threshold) was 0.55 for films, 0.60 for Schick and 0.54 for Sirona, which were not significantly different from each other. Conclusions: Digital images presented better results of interexaminer agreement; however, no additional effect in the diagnostic performance could be observed in comparison to conventional films.
Psychosocial Work Environment Predictors of Short and Long Spells of Registered Sickness Absence During a 2-year Follow Up

Objective: The objective of this study was to investigate the impact of psychosocial work environment factors on short and long absence spells. Methods: Questionnaire data on work environment exposures and registered absence data during 2-year follow up were analyzed with Poisson regression for 1919 employees from the private and public sector. Results: Short spells (1–10 working days) were predicted by low supervisor support, low predictability, and low meaning at work among men and high skill discretion among women. Long spells (>10 days) were predicted by low decision authority, low supervisor support, and low predictability among men and high psychologic demands and low decision authority among women. The variables predictability and meaning at work were developed for this study. Conclusion: Specific psychosocial work environment factors have both common and different effects on short and long absence spells. Effects also differ by gender.
Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean

Spinner dolphins (Stenella longirostris) and spotted dolphins (S. attenuata) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA (mtDNA) have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical levels. Our results showed significant differences between subspecies of spotted (FST: 0.0125; P = 0.0402) and spinner dolphins (FST: 0.0133; P = 0.034), but no support for the division of existing offshore stocks of spotted dolphins or Tres Marias spinner dolphins. We compare these results to previous results of genome-wide nuclear SNP data and suggest high haplotype diversity, female dispersal, male philopatry, or relative power of the two datasets explains the differences observed. Our results further support a genetic basis for biologically meaningful management units at the subspecies level, and provide a critical component to mitigating historical and continued fishery interactions.
Protein Phosphorylation Affects Binding of the Escherichia coli Transcription Activator UhpA to the uhpT Promoter*

Expression of the Escherichia coli sugar phosphate transporter UhpT is induced by extracellular glucose 6-phosphate through a transmembrane signaling process dependent on the sensor kinase UhpB and the UhpT homolog, UhpC. These proteins are thought to regulate the phosphorylation of the transcription activator, UhpA. To examine the effect of protein phosphorylation on the binding of UhpA to target sequences in the uhpT promoter region, the UhpA protein was overexpressed and purified. Purified UhpA was phosphorylated by acetyl phosphate in a reaction that was dependent on Mg2+ and on the presence of aspartate 54, the site of phosphorylation in homologous response regulators. Gel electrophoretic mobility shift and DNase I and hydroxyl radical protection assays showed that UhpA bound specifically to the region of the uhpT promoter extending from −80 to −50 bp, relative to the transcription start site. At higher concentrations of UhpA, binding was extended to the −32 region. Binding to the −64 element exhibited positive cooperativity and was stimulated severalfold by phosphorylation of UhpA, whereas extension to the downstream region was more strongly affected by phosphorylation. The consensus sequences for the high affinity UhpA-binding sites in the −64 element and for the downstream, low affinity sites are proposed. The pattern of in vitro binding by UhpA agreed with the in vivo observations that phosphorylation-independent assembly of the transcription initiation complex can occur at elevated concentrations of UhpA.
Influence of Gynaecologic Adnexal Surgeries on Subsequent Ovarian Function and In Vitro Fertilization Treatment Outcome

Objective To investigate the correlation between gynaecologic adnexal surgery history and pregnancy outcome of in vitro fertilization (IVF) treatment. Methods A total of 810 women who were proceeded 810 IVF treatment cycles from October 2009 to March 2011 were recruited to this retrospective study, based on whether they had history of gynaecologic adnexal surgeries or not. Among 810 women, 587 women had no gynaecologic adnexal surgeries (group A), 223 women had gynaecologic adnexal surgeries (group B). Additionally, the group B was further divided into 4 subgroups based on their different gynaecologic adnexal surgery histories, such as tubal conservative surgery (group Ba1), unilateral salpingectomy (group Ba2), ovarian cyst ablation (group Bb1) and unilateral adnexal resection (group Bb2). The basal levels of FSH, antral follicle count (AFC), clinical pregnancy rate (CPR), embryos implantation rates (IR) and live birth rates (LBR) were compared. Results The levels of FSH and AFC were significantly different between groups A and B, respectively. Therefore, CPR, IR and LBR were significantly lower (P Conclusion The previous history of gynaecologic adnexal surgeries may affect the subsequent ovarian function and also IVF outcomes. As for different operation methods, between tubal conservation surgery and unilateral salpingectomy, the IVF outcomes were not significantly different. The same result we found in different ovarian operation groups.
Genetic evaluation of carcass traits of commercial steers at different slaughter end-points

Hanwoo is a breed of cattle that is native to Korea and has been in use as draft animals for 5,000 years. Compared to Japanese Black cattle, the Hanwoo breed is known for their high marbling, having 15%–23% intramuscular fat (IMF) at final slaughter age (Kim et al., 2005). With regard to carcass value, the marbling score (MS), carcass weight (CWT), eye muscle area (EMA) and back fat thickness (BF) have the greatest influence on profit in the Korean beef industry. The current Hanwoo breeding program has achieved significant rates of genetic gain. For example, an estimate of annual gain over the last 10 years was 8 kg for CWT (2.6% of the average phenotype) and 2.9 cm (3.8%) for EMA (NIAS, 2009). The rate of improvement for CWT was 0.4 based on genetic standards of deviation per year, which is much higher than the gains in MS (0.04 of a genetic standard deviation). Several factors contribute toward the low rate of gain for MS (Lee, 2011, PhD. thesis). Firstly, MS is estimated using a subjective score rather than an objective measurement such as chemical fat percentage. Secondly, candidate bulls (n=400) are selected based on live weight (LWT) and average daily gain (ADG) through performance tests. Both LWT and ADG traits are highly correlated with CWT and EMA, but not with MS. Finally, marbling is a late maturing trait in cattle (Pethick et al., 2005). The premiums for high MS are prompting Korean farmers to extend the finishing period for Hanwoo beyond 30 months to further improve marbling scores. However, Korean proven (KPN) bulls are selected based on the breeding value estimated from carcass data slaughtered at 24 months of age from progeny tests. This may explain why genetic progress in CWT and EMA is much greater than in MS. Currently, the progeny testing evaluation for the selection of KPN occurs every 6 months, and these bulls are distributed across the entire country. It is a well– structured Hanwoo beef production system such as large scale of farm based progeny test that could be re–evaluated breeding value for KPN bulls and cows at different age structure. In the United States of America, most breed associations currently adjust carcass traits to a constant age when computing breeding value, but age is seldom the primary criterion determining slaughter date in the current production systems (Shanks et al., 2001). It could be argued that the estimated carcass quality grade and external fat more closely represent the slaughter criteria. As for the genetic evaluation at different age structures, Cundiff et al. (1969) reported that carcass traits are known to be differently evaluated with different indirect genetic responses according to slaughter end–points, and Koch et al. (1995) reported that slaughter end–points can affect the expression of genetic and environmental differences. Because estimated breeding value is curGenetic Evaluation of Carcass Traits of Commercial Steers at Different Slaughter End–points
Effect of dry period length on milk production in subsequent lactation.

The effect of planned dry period lengths of 4, 7, and 10 wk on subsequent lactational yield was estimated with 366 cows in an experiment in which dry period was manipulated independently of milk yield prior to drying off. In two herds, all three treatments were compared within herd; in six herds, two treatments were compared within herd. Compared with a 7-wk planned dry period, a 3-wk decrease lowered the level of milk production by 2.8 kg of 4% FCM/d in the first 84 d of the subsequent lactation, whereas a 3-wk increase raised the level of milk production by . 5 kg/d. In the first 168 d of the subsequent lactation, the difference between 4-wk and 7-wk planned dry periods was 2.7 kg/d, and the difference between 7- and 10-wk periods was . 4 kg/d. There was no indication of interaction among planned dry period length and lactation number, days open in previous lactation, previous milk yield, breed, or health status with respect to effect on subsequent lactational yield.
European Seasonal and Annual Temperature Variability, Trends, and Extremes Since 1500

Multiproxy reconstructions of monthly and seasonal surface temperature fields for Europe back to 1500 show that the late 20th- and early 21st-century European climate is very likely (>95% confidence level) warmer than that of any time during the past 500 years. This agrees with findings for the entire Northern Hemisphere. European winter average temperatures during the period 1500 to 1900 were reduced by ∼0.5°C (0.25°C for annual mean temperatures) compared to the 20th century. Summer temperatures did not experience systematic century-scale cooling relative to present conditions. The coldest European winter was 1708/1709; 2003 was by far the hottest summer.
Towards Prescriptive Analytics in Cyber-Physical Systems

More and more of our physical world today is being monitored and controlled by so-called cyber-physical systems (CPSs). These are compositions of networked autonomous cyber and physical agents such as sensors, actuators, computational elements, and humans in the loop. Today, CPSs are still relatively small-scale and very limited compared to CPSs to be witnessed in the future. Future CPSs are expected to be far more complex, large-scale, wide-spread, and mission-critical, and found in a variety of domains such as transportation, medicine, manufacturing, and energy, where they will bring many advantages such as the increased efficiency, sustainability, reliability, and security. To unleash their full potential, CPSs need to be equipped with, among other features, the support for automated planning and control, where computing agents collaboratively and continuously plan and control their actions in an intelligent and well-coordinated manner to secure and optimize a physical process, e.g., electricity flow in the power grid. In today’s CPSs, the control is typically automated, but the planning is solely performed by humans. Unfortunately, it is intractable and infeasible for humans to plan every action in a future CPS due to the complexity, scale, and volatility of a physical process. Due to these properties, the control and planning has to be continuous and automated in future CPSs. Humans may only analyse and tweak the system’s operation using the set of tools supporting prescriptive analytics that allows them (1) to make predictions, (2) to get the suggestions of the most prominent set of actions (decisions) to be taken, and (3) to analyse the implications as if such actions were taken. This thesis considers the planning and control in the context of a large-scale multiagent CPS. Based on the smart-grid use-case, it presents a so-called PrescriptiveCPS – which is (the conceptual model of) a multi-agent, multi-role, and multi-level CPS automatically and continuously taking and realizing decisions in near real-time and providing (human) users prescriptive analytics tools to analyse and manage the performance of the underlying physical system (or process). Acknowledging the complexity of CPSs, this thesis provides contributions at the following three levels of scale: (1) the level of a (full) PrescriptiveCPS, (2) the level of a single PrescriptiveCPS agent, and (3) the level of a component of a CPS agent software system. At the CPS level, the contributions include the definition of PrescriptiveCPS,