LLukas22/scidocs huggingface dataset:
Development and validation of genic-SSR markers in sesame by RNA-seq

Sesame (Sesamum indicum L.) is one of the most important oil crops; however, a lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of samples from different sesame growth and developmental stages, and mining of genic-SSR markers to identify valuable markers for sesame molecular genetics research. In this study, 75 bp and 100 bp paired-end RNA-seq was used to sequence 24 cDNA libraries, and 42,566 uni-transcripts were assembled from more than 260 million filtered reads. The total length of uni-transcript sequences was 47.99 Mb, and 7,324 SSRs (SSRs ≥15 bp) and 4,440 SSRs (SSRs ≥18 bp) were identified. On average, there was one genic-SSR per 6.55 kb (SSRs ≥15 bp) or 10.81 kb (SSRs ≥18 bp). Among perfect SSRs (≥18 bp), di-nucleotide motifs (48.01%) were the most abundant, followed by tri- (20.96%), hexa- (25.37%), penta- (2.97%), tetra- (2.12%), and mono-nucleotides (0.57%). The top four motif repeats were (AG/CT)n [1,268 (34.51%)], (CA/TG)n [281 (7.65%)], (AT/AT)n [215 (5.85%)], and (GAA/TTC)n [131 (3.57%)]. A total of 2,164 SSR primer pairs were identified in the 4,440 SSR-containing sequences (≥18 bp), and 300 SSR primer pairs were randomly chosen for validation. These SSR markers were amplified and validated in 25 sesame accessions (24 cultivated accessions, one wild species). 276 (92.0%) primer pairs yielded PCR amplification products in 24 cultivars. Thirty two primer pairs (11.59%) exhibited polymorphisms. Moreover, 203 primer pairs (67.67%) yielded PCR amplicons in the wild accession and 167 (60.51%) were polymorphic between species. A UPGMA dendrogram based on genetic similarity coefficients showed that the correlation between genotype and geographical source was low and that the genetic basis of sesame in China is narrow, as previously reported. The 32 polymorphic primer pairs were validated using an F2 mapping population; 18 primer pairs exhibited polymorphisms between the parents, and 14 genic-SSRs could be integrated into 9 main linkage groups. 2,164 genic-SSR markers have been developed in sesame using transcriptome sequencing. 276 of 300 validated primer pairs successfully yielded PCR amplicons in 24 cultivated sesame accessions. These markers increase current SSR marker resources and will greatly benefit genetic diversity, qualitative and quantitative trait mapping and marker-assisted selection studies in sesame.
New constraints on the provenance of the ANDRILL AND-2A succession (western Ross Sea, Antarctica) from apatite triple dating: APATITE TRIPLE DATING IN ANTARCTICA

[1] Apatite triple dating (fission track, U-Pb and U-Th/He techniques) has been applied to detrital grains from the sedimentary core drilled during the ANDRILL 2A project, which documents the Miocene history of the Victoria Land Basin (western Ross Sea). High-temperature cooling ages show two main clusters (about 30 and 500 Ma) whereas most of low-temperature data are late Oligocene-Early Miocene in age. These latter data are related to the exhumation of the Transantarctic Mountains south of the Discovery Accommodation Zone. Comparison between low-temperature ages suggests that the Transantarctic Mountains have been in a phase of post-orogenic decay since at least 30 Ma. The Oligocene U-Pb data demonstrate the presence of a volcanic event well before the McMurdo volcanic group, whose onset is commonly places at 19 Ma. The location of the volcanic centers is unknown, but they could be below the Ross Ice Shelf south of drilling site. As a whole, these data indicate a major flow of sediments from south to north with only minor contributions from nearby outlet glaciers of the East Antarctic Ice Sheet.
Effect of occlusal plane on smile attractiveness.

OBJECTIVE
To determine the influence of the occlusal plane angle on smile attractiveness as perceived by a group of adult orthodontic patients and dentists.


MATERIALS AND METHODS
The first stage utilized a laboratory approach to record changes in vertical tooth position at different occlusal plane angles using a maxillary model mounted on an articulator. In the second stage, photographic manipulation was undertaken, using data from stage 1, to produce a computerized prediction of the appearance of the smile at differing occlusal plane angles (0, 5, 10, 15, and 20 degrees). Finally, the five developed photographs were assessed by participants.


RESULTS
Alterations in the occlusal plane angle did affect relative smile attractiveness for both patients (n  =  66) and dentists (n  =  66). For patients, the 10 degree smile was rated better than the 0 and 20 degree smiles (P < .01); for dentists, the 15 degree smile was rated better than the 0 and 20 degree smiles (P < .01). The 5, 10, and 15 degree smiles were indistinguishable for patients, and the 10 and 15 degree smiles were indistinguishable for dentists.


CONCLUSION
Changing the occlusal plane angle does affect relative smile attractiveness. However, patients were more tolerant of these changes than dentists. This suggests that large changes in the occlusal plane angle would affect relative smile attractiveness, and small changes are unlikely to affect smile attractiveness.
Cooperative Co-evolutionary Optimization of Software Project Staff Assignments and Job Scheduling

This paper presents an approach to Search Based Software Project Management based on Cooperative Co-evolution. Our approach aims to optimize both developers’ team staffing and work package scheduling through cooperative co-evolution to achieve early overall completion time. To evaluate our approach, we conducted an empirical study, using data from four real-world software projects. Results indicate that the Co-evolutionary approach significantly outperforms a single population evolutionary algorithm. Cooperative co-evolution has not previously been applied to any problem in Search Based Software Engineering (SBSE), so this paper reports the first application of cooperative coevolution in the SBSE literature. We believe that co-evolutionary optimization may fit many applications in other SBSE problem domains, since software systems often have complex inter-related subsystems and are typically characterized by problems that need to be co-evolved to improve results.
Changes in basal and postmethionine load concentrations of total homocysteine and cystathionine after B vitamin intervention.

BACKGROUND
Vitamin B-6 is necessary for the metabolism of homocysteine and is often used in combination with folic acid and vitamin B-12 in clinical trials that investigate whether the lowering of plasma total homocysteine (tHcy) can prevent vascular disease.


OBJECTIVE
We compared the effects of vitamin B-6 with the effects of folic acid and vitamin B-12, as used in the Western Norway B-vitamin Intervention Trial (WENBIT), on basal and postmethionine load (PML) tHcy and cystathionine concentrations.


DESIGN
Ninety patients with suspected coronary artery disease were randomly assigned to 1 of 4 groups to receive daily oral treatment with 1) 0.8 mg folic acid, 0.4 mg vitamin B-12, and 40 mg vitamin B-6 (group A); 2) 0.8 mg folic acid and 0.4 mg vitamin B-12 (group B); 3) 40 mg vitamin B-6 (group C); or 4) placebo (group D). For the first 2 wk, groups A and B received additional folic acid (5 mg/d). A methionine-loading test was performed at baseline and after 3 mo.


RESULTS
Treatment with folic acid and vitamin B-12 caused a rapid and significant lowering of basal (31%) and PML tHcy concentrations (22%), with no effect on cystathionine. Vitamin B-6 did not change basal tHcy and had a significant but limited effect on PML tHcy concentrations. However, vitamin B-6 treatment markedly lowered basal and PML cystathionine by 31% and 42%, respectively.


CONCLUSION
The folic acid and vitamin B-12 combination applied in WENBIT provides rapid, substantial, and long-term tHcy-lowering effects, whereas the effect of vitamin B-6 on tHcy was relatively small and confined to PML tHcy. However, vitamin B-6 treatment caused a marked reduction in plasma cystathionine. Cystathionine could be a useful marker for assessment of the vitamin B-6 effect and should, together with tHcy, be related to clinical outcome in ongoing trials.
The Tokuhashi score: significant predictive value for the life expectancy of patients with breast cancer with spinal metastases.

STUDY DESIGN
Retrospective study of 55 consecutive patients with spinal metastases secondary to breast cancer who underwent surgery.


OBJECTIVE
To evaluate the predictive value of the Tokuhashi score for life expectancy in patients with breast cancer with spinal metastases.


SUMMARY OF BACKGROUND DATA
The score, composed of 6 parameters each rated from 0 to 2, has been proposed by Tokuhashi and colleagues for the prognostic assessment of patients with spinal metastases.


METHODS
A total of 55 patients surgically treated for vertebral metastases secondary to breast cancer were studied. The score was calculated for each patient and, according to Tokuhashi, the patients were divided into 3 groups with different life expectancy according to their total number of scoring points. In a second step, the grouping for prognosis was modified to get a better correlation of the predicted and definitive survival.


RESULTS
Applying the Tokuhashi score for the estimation of life expectancy of patients with breast cancer with vertebral metastases provided very reliable results. However, the original analysis by Tokuhashi showed a limited correlation between predicted and real survival for each prognostic group. Therefore, our patients were divided into modified prognostic groups regarding their total number of scoring points, leading to a higher significance of the predicted prognosis in each group (P < 0.0001), and a better correlation of the predicted and real survival.


CONCLUSION
The modified Tokuhashi score assists in decision making based on reliable estimators of life expectancy in patients with spinal metastases secondary to breast cancer.
Exploring high-intensity QED at ELI

We give a non-technical overview of QED effects arising in the presence of ultra-strong electromagnetic fields highlighting the new prospects provided by a realisation of the ELI laser facility.
ON A SUGGESTION RELATING TOPOLOGICAL AND QUANTUM MECHANICAL ENTANGLEMENTS

We analyze a recent suggestion [New J. Phys. 4 (2002) 73], [quant-ph/0304091] on a possible relation between topological and quantum mechanical entanglements. We show that a one to one correspondence does not exist, neither between topologically linked diagrams and entangled states, nor between braid operators and quantum entanglers. We also add a new dimension to the question of entangling properties of unitary operators in general.
Detection of Rheumatoid Arthritis-Interstitial Lung Disease Is Enhanced by Serum Biomarkers.

RATIONALE
Interstitial lung disease (ILD), a leading cause of morbidity and mortality in rheumatoid arthritis (RA), is highly prevalent, yet RA-ILD is underrecognized.


OBJECTIVES
To identify clinical risk factors, autoantibodies, and biomarkers associated with the presence of RA-ILD.


METHODS
Subjects enrolled in Brigham and Women's Hospital Rheumatoid Arthritis Sequential Study (BRASS) and American College of Rheumatology (ACR) cohorts were evaluated for ILD. Regression models were used to assess the association between variables of interest and RA-ILD. Receiver operating characteristic curves were generated in BRASS to determine if a combination of clinical risk factors and autoantibodies can identify RA-ILD and if the addition of investigational biomarkers is informative. This combinatorial signature was subsequently tested in ACR.


MEASUREMENTS AND MAIN RESULTS
A total of 113 BRASS subjects with clinically indicated chest computed tomography scans (41% with a spectrum of clinically evident and subclinical RA-ILD) and 76 ACR subjects with research or clinical scans (51% with a spectrum of RA-ILD) were selected. A combination of age, sex, smoking, rheumatoid factor, and anticyclic citrullinated peptide antibodies was strongly associated with RA-ILD (areas under the curve, 0.88 for BRASS and 0.89 for ACR). Importantly, a combinatorial signature including matrix metalloproteinase 7, pulmonary and activation-regulated chemokine, and surfactant protein D significantly increased the areas under the curve to 0.97 (P = 0.002, BRASS) and 1.00 (P = 0.016, ACR). Similar trends were seen for both clinically evident and subclinical RA-ILD.


CONCLUSIONS
Clinical risk factors and autoantibodies are strongly associated with the presence of clinically evident and subclinical RA-ILD on computed tomography scan in two independent RA cohorts. A biomarker signature composed of matrix metalloproteinase 7, pulmonary and activation-regulated chemokine, and surfactant protein D significantly strengthens this association. These findings may facilitate identification of RA-ILD at an earlier stage, potentially leading to decreased morbidity and mortality.
The risk of new onset depression in association with influenza – A population-based observational study

IMPORTANCE
Case-reports provided evidence that influenza infections, particularly severe episodes, may exert neuronal damage in the CNS and thereby increase the risk of depression.


OBJECTIVE
It was the aim of this study to analyse the association between influenza infections and the risk of developing incident depression.


DESIGN
We conducted a case-control analysis between 2000 and 2013 using the large UK-based primary care database Clinical Practice Research Datalink (CPRD).


SETTING
This database contains anonymous longitudinal data from primary care. At present, it contains over 100 million person-years of data from some 10 million active patients.


PARTICIPANTS
We encompassed 103307 patients below the age of 80 years with an incident major depression diagnosis between 2000 and 2013, and matched each case to one control patient on age, sex, general practice, number of medical encounters, and years of history in the CPRD prior to the index date.


EXPOSURE
Major depression diagnosis was identified by READ-codes based on ICD-10 codes (F32), with a minimum of three prescriptions for antidepressant drugs recorded after the diagnosis.


MAIN OUTCOME
We calculated relative risk estimates of developing depression in association with previous influenza infections, stratified by the number, timing and severity of such events, and we adjusted for a variety of comorbidities, smoking status, alcohol intake, body mass index, use of oral corticosteroids, and benzodiazepines.


RESULTS
Patients with a previous influenza infection had an increased risk of developing depression (OR 1.30, 95%CI 1.25-1.34) compared to patients with no history of influenza infections. A recent influenza infection recorded within 30-180 days prior to the index date yielded an adjusted 1.57 (95%CI 1.36-1.81), and an increasing number of previous influenza infections was associated with increasing odds ratios (⩾ 3 recorded influenza infections, adjusted OR 1.48, 95%CI 1.22-1.81).


CONCLUSION
This study suggests that influenza infections are associated with a moderately increased risk of developing depression.
Lateral Brow Lift: A Multi-Point Suture Fixation Technique

BACKGROUND
Descent of the lateral aspect of the brow is one of the earliest signs of aging. The purpose of this study was to describe an open surgical technique for lateral brow lifts, with the goal of achieving reliable, predictable, and long-lasting results.


METHODS
An incision was made behind and parallel to the temporal hairline, and then extended deeper through the temporoparietal fascia to the level of the deep temporal fascia. Dissection was continued anteriorly on the surface of the deep temporal fascia and subperiosteally beyond the temporal crest, to the level of the superolateral orbital rim. Fixation of the lateral brow and tightening of the orbicularis oculi muscle was achieved with the placement of sutures that secured the tissue directly to the galea aponeurotica on the lateral aspect of the incision. An additional fixation was made between the temporoparietal fascia and the deep temporal fascia, as well as between the temporoparietal fascia and the galea aponeurotica. The excess skin in the temporal area was excised and the incision was closed.


RESULTS
A total of 519 patients were included in the study. Satisfactory lateral brow elevation was obtained in most of the patients (94.41%). The following complications were observed: total relapse (n=8), partial relapse (n=21), neurapraxia of the frontal branch of the facial nerve (n=5), and limited alopecia in the temporal incision (n=9).


CONCLUSIONS
We consider this approach to be a safe and effective procedure, with long-lasting results.
Skin-to-skin care with the father after cesarean birth and its effect on newborn crying and prefeeding behavior.

BACKGROUND
Previous reports have shown that skin-to-skin care immediately after vaginal birth is the optimal form of care for full-term, healthy infants. Even in cases when the mother is awake and using spinal analgesia, early skin-to-skin contact between her and her newborn directly after cesarean birth might be limited for practical and medical safety reasons. The aim of the present study was to compare the effects of skin-to-skin contact on crying and prefeeding behavior in healthy, full-term infants born by elective cesarean birth and cared for skin-to-skin with their fathers versus conventional care in a cot during the first 2 hours after birth.


METHODS
Twenty-nine father-infant pairs participated in a randomized controlled trial, in which infants were randomized to be either skin-to-skin with their father or next to the father in a cot. Data were collected both by tape-recording crying time for the infants and by naturalistic observations of the infants' behavioral response, scored every 15 minutes based on the scoring criteria described in the Neonatal Behavioral Assessment Scale (NBAS).


RESULTS
The primary finding was the positive impact the fathers' skin-to-skin contact had on the infants' crying behavior. The analysis of the tape recordings of infant crying demonstrated that infants in the skin-to-skin group cried less than the infants in the cot group (p<0.001). The crying of infants in the skin-to-skin group decreased within 15 minutes of being placed skin-to-skin with the father. Analysis of the NBAS-based observation data showed that being cared for on the father's chest skin-to-skin also had an impact on infant wakefulness. These infants became drowsy within 60 minutes after birth, whereas infants cared for in a cot reached the same stage after 110 minutes. Rooting activity was more frequent in the cot group than in the skin-to-skin group (p<0.01), as were sucking activities (p<or=0.001) and overall duration of wakefulness (p<0.01).


CONCLUSIONS
The infants in the skin-to-skin group were comforted, that is, they stopped crying, became calmer, and reached a drowsy state earlier than the infants in the cot group. The father can facilitate the development of the infant's prefeeding behavior in this important period of the newborn infant's life and should thus be regarded as the primary caregiver for the infant during the separation of mother and baby.
StakeSource2.0: using social networks of stakeholders to identify and prioritise requirements

Software projects typically rely on system analysts to conduct requirements elicitation, an approach potentially costly for large projects with many stakeholders and requirements. This paper describes StakeSource2.0, a web-based tool that uses social networks and collaborative filtering, a "crowdsourcing" approach, to identify and prioritise stakeholders and their requirements.
Reading behavior in the digital environment: Changes in reading behavior over the past ten years

Purpose – This study attempts to investigate reading behavior in the digital environment by analyzing how people’s reading behavior has changed over the past ten years. Design/methodology/approach – Survey and analysis methods are employed. Findings – With an increasing amount of time spent reading electronic documents, a screen-based reading behavior is emerging. The screen-based reading behavior is characterized by more time spent on browsing and scanning, keyword spotting, one-time reading, non-linear reading, and reading more selectively, while less time is spent on in-depth reading, and concentrated reading. Decreasing sustained attention is also noted. Annotating and highlighting while reading is a common activity in the printed environment. However, this “traditional” pattern has not yet migrated to the digital environment when people read electronic documents. Originality/value – Implications for the changes in reading behavior are discussed, and directions for future research are suggested.
The importance of phase in signals

In the Fourier representation of signals, spectral magnitude and phase tend to play different roles and in some situations many of the important features of a signal are preserved if only the phase is retained. Furthermore, under a variety of conditions, such as when a signal is of finite length, phase information alone is sufficient to completely reconstruct a signal to within a scale factor. In this paper, we review and discuss these observations and results in a number of different contexts and applications. Specifically, the intelligibility of phase-only reconstruction for images, speech, and crystallographic structures are illustrated. Several approaches to justifying the relative importance of phase through statistical arguments are presented, along with a number of informal arguments suggesting reasons for the importance of phase. Specific conditions under which a sequence can be exactly reconstructed from phase are reviewed, both for one-dimensional and multi-dimensional sequences, and algorithms for both approximate and exact reconstruction of signals from phase information are presented. A number of applications of the observations and results in this paper are suggested.
Economic and Disease Burden of Dengue in Southeast Asia

BACKGROUND
Dengue poses a substantial economic and disease burden in Southeast Asia (SEA). Quantifying this burden is critical to set policy priorities and disease-control strategies.


METHODS AND FINDINGS
We estimated the economic and disease burden of dengue in 12 countries in SEA: Bhutan, Brunei, Cambodia, East-Timor, Indonesia, Laos, Malaysia, Myanmar, Philippines, Singapore, Thailand, and Viet Nam. We obtained reported cases from multiple sources--surveillance data, World Health Organization (WHO), and published studies--and adjusted for underreporting using expansion factors from previous literature. We obtained unit costs per episode through a systematic literature review, and completed missing data using linear regressions. We excluded costs such as prevention and vector control, and long-term sequelae of dengue. Over the decade of 2001-2010, we obtained an annual average of 2.9 million (m) dengue episodes and 5,906 deaths. The annual economic burden (with 95% certainty levels) was US$950m (US$610m-US$1,384m) or about US$1.65 (US$1.06-US$2.41) per capita. The annual number of disability-adjusted life years (DALYs), based on the original 1994 definition, was 214,000 (120,000-299,000), which is equivalent to 372 (210-520) DALYs per million inhabitants.


CONCLUSION
Dengue poses a substantial economic and disease burden in SEA with a DALY burden per million inhabitants in the region. This burden is higher than that of 17 other conditions, including Japanese encephalitis, upper respiratory infections, and hepatitis B.
A modal control for active/semi-active suspension systems

Active/semi-active suspension systems are getting widely accepted for their potential to improve ride comfort of passenger cars with respect to traditional suspension systems. A feedback controller has been designed allowing to control separately the vehicle body motions of heave, pitch and roll taking into account the dynamics of the active/semi-active actuator. Simulations results stated that significant improvements of ride comfort can be achieved respect to passive shock absorbers.