Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals

Amplified fragment length polymorphisms (AFLP) are dominant markers frequently used to build linkage maps where heterozygosity could be inferred by a backcross breeding strategy. In the present study, we describe the utilization of an unmanipulated great reed warbler, Acrocephalus arundinaceus pedigree to infer heterozygous genotypes of AFLP markers in order to map these markers to a partial linkage map previously based on microsatellites. In total, 50 of the 83 autosomal AFLPs (60%) and 4 of 5 Z‐linked AFLPs (80%) were mapped. For each marker, on average, 88% of the expected number of heterozygote parents was detected. The likelihood of map assignment was to a large extent due to the number and density of microsatellite markers already in the map. The ‘parsimonious linkage map’, that is the map based on the most parsimonious location of all significantly linked markers, consisted of 21 autosomal linkage groups with 2 to 15 markers and had a total map size of 552 cM in males and 858 cM in females. The Z‐chromosome linkage group with 12 markers had a size of 155 cM. The autosomal ‘framework linkage map’, that is the map based only on markers with an unambiguous position, had a total size of 237 cM in males and 440 cM in females, respectively. The inclusion of AFLPs enlarged the previous map substantially (e.g. the autosomal parsimonious linkage map became 441 cM and 621 cM larger for male and female recombination, respectively). The probability that an AFLP became mapped increased with increasing level of heterozygosity, whereas the probability of mapping into a framework position increased with both heterozygosity and number of genotyped individuals. Our results suggest that AFLP provides a fast and inexpensive means of enlarging genetic maps already composed of markers with high polymorphism, also in wild populations with unmanipulated pedigrees.
A Formant Frequency Estimation Scheme for Speech Signals in the Presence of Noise

In this paper, a new scheme for the estimation of formant frequencies of noise-corrupted speech signals is presented. A once-repeated autocorrelation function (ORACF) of the observed noisy speech signal is proposed to employ in a linear predictive based formant estimation method. It has been shown that the ORACF is capable of reducing the effect of additive noise significantly and if, instead of conventional ACF, ORACF is used in a modified form of least-squares Yule-Walker equations, a better performance in the formant estimation is achieved. Moreover, a frequency-domain algorithm is incorporated in the proposed scheme to avoid the possible estimation error in extracting a formant with low energy. The proposed algorithm has been tested on synthetic and natural vowels as well as some naturally spoken sentences in the presence of additive noise. The experimental results demonstrate a better performance obtained by the proposed scheme in comparison to some of the existing methods at low levels of signal-to-noise ratio (SNR).
A Priori Risk and Optimal Test Accuracy in Prenatal Diagnostics

The prevalence of fetal chromosome anomalies rises exponentially with the age of the pregnant woman. The risk of fetal anomalies can be specified using biochemical screening tests such as the triple test. This test substantially reduces the number of amniocenteses and proportionally the number of procedure-related miscarriages. However, disadvantages of the triple test include the utility loss of pregnant women who, following a false-negative test result, do not undergo amniocentesis and bear a disabled child as well as the intangible cost of a false-positive triple test. This paper employs a decision-analytic model to reveal the evaluation of this tradeoff, which is implicitly fixed by policy recommendations for a direct amniocentesis at maternal age of 35. It then determines the optimal level of cutoff risk for the triple test, and derives comparative static results: the optimal test accuracy decreases with increasing a-priori risk and increases with a rise in the miscarriage risk and in the woman's preference for detecting an affected fetus as compared to avoiding a miscar-riage of an unaffected fetus. These results are in contrast to current clinical practice, where the cutoff of the triple test usually remains fixed.
Prophylaxis against Neisseria meningitidis infections and antibody responses in patients with deficiency of the sixth component of complement.

Forty South African patients with homozygous deficiency of the sixth component of complement (C6) have been identified in an area where group B meningococcal meningitis is endemic; 22 of the 24 proband cases presented with recurrent meningococcal meningitis. In a 2- to 4-year prospective study, patients with recurrent infections who received monthly prophylactic long-acting penicillin were significantly protected from subsequent neisserial infection compared with those who did not receive penicillin (P = .02, Fisher's exact test). Heterogeneous susceptibility to neisserial infection was confirmed by following C6-deficient patients who presented with one or no Neisseria meningitidis infections. These patients, on no prophylaxis, had significantly fewer infections (P = .004) than did patients who presented with recurrent disease. Functional C6 activity was restored by transfusion of fresh frozen plasma in a C6-deficient patient resistant to conventional antibiotic treatment. Antibody levels to the serotype 2 outer membrane proteins were significantly elevated in C6-deficient patients compared with control groups (P = .001).
Male-Female Wage Differentials in Japan

The report issued by the Labor Standards Act Study Group in November 1978 met with a strong reaction in many quarters. One of the reasons seems to be a point it made regarding factors in wage differentials between male and female workers, namely, that "among the special measures for women, …to retain even those that no longer have a rationale may, rather than protect women, narrow their occupational choices. " (1)
Creative Diversity: Expanding Software for 3D Human Avatar Design

This extended abstract describes research that designs 3D human avatar generation software for amateur creative users. Currently available software relies on limiting the range of possible bodies that the user is able to create, within the boundaries of normative physicality, in order to simplify interaction for users without 3D modeling skills. Rather than artificially limiting user output, we are creating open source software that expands the range of bodies able to be represented in program, following a user centered design process to implement direct manipulation techniques extrapolated from artistic practice. This paper describes the background context, aims, and current research activities related to creating this software.
Response of the Cultivated Tomato and Its Wild Salt-tolerant Relative Lycopersicon Pennellii to Salt-dependent Oxidative Stress: Increased Activities of Antioxidant Enzymes in Root Plastids

Root plastids of the cultivated tomato Lycopersicon esculentum (Lem) exhibited salt-induced oxidative stress as indicated by the increased H 2 O 2 and lipid peroxidation levels which were accompanied with increased contents of the oxidized forms of ascorbate and glutathione. In contrast, H 2 O 2 level decreased, lipid peroxidation level slightly decreased and the levels of the reduced forms of ascorbate and glutathione increased in plastids of L. pennellii (Lpa) species in response to salinity. This better protection of Lpa root plastids from salt-induced oxidative stress was correlated with increased activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidases (POD), monodehydroascorbate reductase (MDHAR), glutathione peroxidase (GPX), glutathione- S -transferase (GST) and phospholipid hydroperoxide glutathione peroxidase (PHGPX). In the plastids of both species, activities of SOD, APX, and POD could be resolved into several isozymes. In Lem plastids two Cu/ZnSOD isozymes were found whereas in Lpa an additional FeSOD type could also be detected. In response to salinity, activities of selected SOD, APX, and POD isozymes were increased in Lpa, while in Lem plastids the activities of most of SOD and POD isozymes decreased. Taken together, it is suggested that plastids play an important role in the adaptation of Lpa roots to salinity.
The Utility of Outpatient Commitment: II. Mortality Risk and Protecting Health, Safety, and Quality of Life.

OBJECTIVE This study assessed the contribution of a form of outpatient commitment-community treatment orders (CTOs)-to mortality risk and quality of life of patients with severe mental illness. METHODS Data (2000--2012) were obtained from the Australian National Death Index, Victoria Department of Health, Victoria police records, and National Outcomes and CaseMix Collection quality-of-life records for patients in the Victorian Psychiatric Case Register/RAPID with a history of psychiatric hospitalization: CTO cohort, N=11,424; non-CTO cohort, N=16,161. The contribution of CTOs to mortality risk associated with CTO facilitation of access to general medical care and prevention of criminal involvement was assessed with logistic regression models. Cohort differences in quality of life were also examined. RESULTS A total of 2,727 patients (10%) in the overall sample died, and the sample had a higher mortality risk than the general population. Probability of death by any cause was 9% lower in the CTO cohort than in the non-CTO cohort. Facilitation of access to medical care accounted for a 20% reduction in risk of non-injury-related deaths in the CTO cohort, compared with the non-CTO cohort. Risk of death by self-harm was 32% higher, compared with the non-CTO cohort. CTO placement appeared to lead to a gain of 3.8 years of life among men and 2.4 years among women, compared with the non-CTO cohort. Quality-of-life scores were modestly less favorable for the non-CTO cohort. CONCLUSIONS CTO placement was associated with lower mortality risk via facilitated access to medical care and with modest enhancement of quality of life.
Throughput Scaling in Cognitive Multiple Access Networks with Power and Interference Constraints

This paper focuses on the secondary network throughput scaling in cognitive radio networks when secondary users' transmission powers are optimally allocated. Throughput scaling laws are obtained for two different cognitive radio networks under two different communication scenarios. In the first network type called power-interference limited networks, secondary users' transmission powers are limited by both individual average power constraints and the constraint on the average interference that they cause to primary users. In the second network type called interference limited networks, secondary users' transmission powers are only limited by average interference constraint. For both network types, an asymmetric communication scenario, in which the channels between secondary users and the secondary base station experience Rayleigh fading and those between secondary users and the primary base station experience Rician fading, and a symmetric communication scenario, in which both types of channels experience Rayleigh fading, are considered. It is shown that the secondary network throughput scales like loglog((K+1)/exp(K)*N) and log((K+1)/exp(K)*N) for power-interference limited and interference limited networks, respectively, under the asymmetric communication scenario, where N is the number of secondary users and K > 0 is the Rician factor. For the symmetric communication scenario, these scaling laws are given by loglog(N) and log(N) for power-interference limited and interference limited networks, respectively.
Bronchial wall thickness: appropriate window settings for thin-section CT and radiologic-anatomic correlation.

PURPOSE To analyze the influence of computed tomographic (CT) window settings on bronchial wall thickness and to define appropriate window settings for its evaluation. MATERIALS AND METHODS Three inflation-fixed lungs were scanned with a section thickness of 1.5 mm by using a high-spatial-frequency algorithm. Wall thickness in 10 bronchial specimens was measured with planimetry. Window centers were altered in a range of -200 to -900 HU and window widths in a range of 400-1,500 HU. Relative and absolute differences between CT and planimetric values were calculated. CT and planimetric measures were correlated. Inter- and intraobserver variabilities were determined. RESULTS Window widths less than 1,000 HU resulted in a substantial overestimation of bronchial wall thickness, whereas widths greater than 1,400 HU resulted in an underestimation of bronchial wall thickness. There was no interaction between "width" and "center" regarding their influence on bronchial walls (F = 0.23; P = .99). Correlation between CT and planimetry was statistically significant (r = .85; P = .0001). Differences between the two observers were not statistically significant; results of the measurements of the two observers correlated well (r = .97; P = .001). CONCLUSION Bronchial wall thickness on thin-section CT scans should be evaluated with window centers between -250 and -700 HU and with window widths greater than 1,000 HU. Other than window settings, notably window widths less than 1,000 HU, can lead to substantial artificial thickening of bronchial walls.
Semiconductor nanolasers

Semiconductor nanolasers represent the current frontier of research in the confluencing area of nanotechnology (or nanophotonics) and semiconductor lasers. In this paper, we review some of the most exciting progress made recently in the area. We will focus on nanoscale lasers made of semiconductor nanowires grown in a bottom‐up fashion or nanopillars that are produced through a top‐down wafer etching. Special features of these nanolasers will be reviewed. In particular, recent results on metal–semiconductor plasmonic lasers will be presented which represents the smallest lasers by taking advantages of surface plasmonic effects. Due to the small size and strong confinement in these nanolasers, certain familiar concepts in semiconductor‐laser physics need to be re‐examined to determine their validity or implication at nanoscale. These include the concept of modal gain and confinement factor (CF). The seemly abnormal behavior of CF in dielectric and plasmonic nanolasers will be explained from a unified point of view. Throughout this tutorial, we attempt to address the question of how small a laser can be made or whether there exists an ultimate size limit for a laser.
Effects of a collagen matrix containing basic fibroblast growth factor on wound contraction.

We evaluated the effectiveness of basic fibroblast growth factor (bFGF) in inhibiting wound contraction, both alone and in combination with collagen matrix, using a simulated in vivo delayed healing type model. We also studied the mechanisms involved in this inhibition in in vitro experiments using fibroblast populated collagen gels. As a result, we were able to demonstrate that both collagen matrix and bFGF significantly inhibited wound contraction; especially, bFGF acted in a dose-dependent fashion. Interestingly, their combination was much more effective than either collagen matrix or bFGF alone, a finding that was supported by the histopathological data. Wounds treated with collagen matrix, but not control wounds, showed horizontal rearrangement of collagen fibers in dermis as well as evidence of fibroblast proliferation, which was not observed in scar regions surrounded by normal dermis. Using fibroblast-populated collagen gel contraction as an in vitro model, we found that bFGF significantly inhibited contraction. Taking all these results together, it was concluded that collagen matrix is useful not only as a carrier of cytokines such as bFGF, but also for the quick closure of chronic wounds, thereby preventing contracture, which remains one of the most challenging problems in treating this type of wound. Application of bFGF-treated collagen matrix to chronic wounds such as decubitus, and diabetic and leg ulcers may prove to be highly beneficial in clinical practice.
Total, caffeinated and decaffeinated coffee and tea intake and gastric cancer risk: Results from the EPIC cohort study

Prospective studies examining the association between coffee and tea consumption and gastric cancer risk have shown inconsistent results. We investigated the association between coffee (total, caffeinated and decaffeinated) and tea consumption and the risk of gastric cancer by anatomical site and histological type in the European Prospective Investigation into Cancer and Nutrition study. Coffee and tea consumption were assessed by dietary questionnaires at baseline. Adjusted hazard ratios (HRs) were calculated using Cox regression models. During 11.6 years of follow up, 683 gastric adenocarcinoma cases were identified among 477,312 participants. We found no significant association between overall gastric cancer risk and consumption of total coffee (HR 1.09, 95%‐confidence intervals [CI]: 0.84–1.43; quartile 4 vs. non/quartile 1), caffeinated coffee (HR 1.14, 95%‐CI: 0.82–1.59; quartile 4 vs. non/quartile 1), decaffeinated coffee (HR 1.07, 95%‐CI: 0.75–1.53; tertile 3 vs. non/tertile 1) and tea (HR 0.81, 95%‐CI: 0.59–1.09; quartile 4 vs. non/quartile 1). When stratified by anatomical site, we observed a significant positive association between gastric cardia cancer risk and total coffee consumption per increment of 100 mL/day (HR 1.06, 95%‐CI: 1.03–1.11). Similarly, a significant positive association was observed between gastric cardia cancer risk and caffeinated coffee consumption (HR 1.98, 95%‐CI: 1.16–3.36, p‐trend=0.06; quartile 3 vs. non/quartile 1) and per increment of 100 mL/day (HR 1.09, 95%‐CI: 1.04–1.14). In conclusion, consumption of total, caffeinated and decaffeinated coffee and tea is not associated with overall gastric cancer risk. However, total and caffeinated coffee consumption may be associated with an increased risk of gastric cardia cancer. Further prospective studies are needed to rule out chance or confounding.
Detection of Border Disease Virus in Fetuses, Stillbirths, and Newborn Lambs from Natural and Experimental Infections

The purpose of the present study was to evaluate the use of enzyme-linked immunosorbent assay (ELISA) antigen detection in blood or fetal fluids and reverse transcription polymerase chain reaction (RT-PCR) amplification in tissues for routine laboratory diagnosis of Border disease virus (BDV) infection. Samples from 67 fetuses, 6 stillbirths, and 11 lambs from 25 commercial flocks with suspicion of BDV abortion and 3 fetuses, 7 stillbirths, and 15 lambs obtained from an experimental infection with a local isolate (BDV genotype 4) were investigated. Presence of BDV was detected by RT-PCR in 7.9% of fetuses, 50% of stillbirths, and 50% of lambs from the commercial flocks analyzed, corresponding to 8 of the 25 farms (32%). A similar percentage of the lambs and stillbirths from the experimental infection were positive by RT-PCR of tissue samples (54.5%), and the highest positivity was detected in lymph node, thyroid gland, and kidney. The current study revealed that RT-PCR analysis of stillbirths and lambs with clinical symptoms is more suitable than the analysis of fetuses to confirm the presence of BDV in a flock. Pestiviral antigen was detected by antigen ELISA in a high proportion of fetuses (24/58) and stillbirths (3/4) from commercial flocks, but in lambs, the presence of colostral antibodies masked the detection of the antigen by ELISA. Nevertheless, in lambs from the experimental infection that were not fed colostrum, antigen ELISA was less efficient than RT-PCR in detecting viral presence in stillbirths and lambs. Antigen ELISA is therefore recommended for fetuses with advanced autolysis that can adversely affect RNA integrity.
Synthesis of Isochromene-Type Scaffolds via Single-Flask Diels–Alder-[4 + 2]-Annulation Sequence of a Silyl-Substituted Diene with Menadione

A sequential Diels–Alder reaction/silicon-directed [4 + 2]-annulation was developed to assemble hydroisochromene-type ring systems from menadione 2. In the first step, a Diels–Alder of the 1-silyl-substituted butadiene 1 with 2 furnished an intermediate cyclic allylsilane. Subsequently, TMSOTf promoted a [4 + 2]-annulation through trapping of an oxonium, generated by condensation between an aldehyde and the TBS protected alcohol resulted in the formation of a cis-fused hydroisochromene 13.
Optimal Pesticide Scheduling in Precision Agriculture

Agricultural automation presents challenges typically encountered in the realm of cyber-physical systems, such as incomplete information (plant health indicators), external disturbances (weather), limited control authority (fertilizers cannot make a plant mature arbitrarily fast), and a combination of discrete events and continuous plant dynamics. In this paper, we investigate the problem of optimal pesticide spray scheduling. Regulations impose strict requirements on scheduling, e.g., individual pesticides are only effective during certain seasons and pesticides cannot be sprayed too close to harvest time. We show how to translate these requirements to a metric temporal logic formula over the space of schedules. We next use the theory of optimal mode scheduling to generate a schedule that minimizes the risk of various infestations over time while guaranteeing the satisfaction of the constraints. We demonstrate this methodology via simulation with scheduling constraints based on recommendations and regulations from agricultural experts. Our case study considers blueberries, a crop whose cultivation currently involves little automation.
The burden of new‐onset diabetes mellitus after transplantation

Abstract: The clinical impact of new‐onset diabetes mellitus (NODM) is frequently underestimated by clinicians. NODM occurs in approximately 15–20% of renal transplant patients and 15% of liver transplant recipients. Diabetes after transplantation is a leading risk factor for cardiovascular events, with a higher prognostic value than in the non‐transplant population. NODM also appears to have a negative influence on graft function, and graft survival rates after renal transplantation are significantly lower in patients who develop diabetes than in controls. Patient mortality following renal transplantation is generally found to be higher in patients with NODM, due to increased cardiovascular and peripheral vascular disease, accelerated graft deterioration and diabetes‐related complications, notably infection. A renal registry analysis has reported an increase of 87% in risk of death following onset of NODM. There is also limited evidence that NODM is associated with increased risk of death in liver transplant patients. The relative incidence and severity of diabetic complications in transplant recipients have not been assessed rigorously in a clinical trial but registry data indicate that 20% of renal transplant patients with NODM experience at least one clinically significant diabetic complication within three years. Financially, the additional healthcare costs incurred over the first two years following onset of NODM amount to $21 500. Routine pre‐transplant assessment of diabetic risk, with requisite modification of lifestyle, glycaemic monitoring and immunosuppressive regimens, and coupled with standardized, aggressive hypoglycaemic management as necessary, offers an important opportunity to alleviate the burden of NODM for transplant patients.