Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian inference for normal multiple-trait individual-tree models with missing records via full conjugate Gibbs

In forest genetics, restricted maximum likelihood (REML) estimation of (co)variance components from nor- mal multiple-trait individual-tree models is affected by the absence of observations in any trait and individual. Missing records affect the form of the distribution of REML estimates of genetics parameters, or of functions of them, and the estimating equations are computationally involved when several traits are analysed. An alternative to REML estimation is a fully Bayesian approach through Markov chain Monte Carlo. The present research describes the use of the full conjugate Gibbs algorithm proposed by Cantet et al. (R.J.C. Cantet, A.N. Birchmeier, and J.P. Steibel. 2004. Genet. Sel. Evol. 36: 49-64) to estimate (co)variance components in multiple-trait individual-tree models. This algorithm con- verges faster to the marginal posterior densities of the parameters than regular data augmentation from multivariate nor- mal data with missing records. An expression to calculate the deviance information criterion for the selection of linear parameters in normal multiple-trait models is also given. The developments are illustrated by means of data from dif- ferent crosses of two species of Pinus.
Giant folliculosebaceous cystic hamartoma of the vulva: A rare occurrence

Folliculosebaceous cystic hamartoma (FSCH) is a rare, benign, slow-growing papulonodular cutaneous lesion that usually occurs on the scalp and face but in some rare cases can emerge on the extremities or torso. Genital involvement is extremely uncommon. Pathologically, they are composed of dilated follicular and sebaceous elements of the skin along with mesenchymal elements. Giant FSCH of the vulva can be disfiguring, leading to sexual and psychological issues affecting quality of life (QOL), as happened in the present case. Ethical approval for this study was obtained from the local institutional ethics committee (Manipal Academy of Higher Education). The patient provided informed consent for the present study.
Sex- and age-specific mild cognitive impairment is associated with low hand grip strength in an older Chinese cohort

Background Few studies have demonstrated the impact of characteristics like age and sex on the association between hand grip strength (HGS) and mild cognitive impairment (MCI). In this cross-sectional study, we aimed to examine the effects of sex and age on the relationship between HGS and MCI. Methods We enrolled older adults age ≥60 years (n = 1009) and measured HGS and MCI in all participants. We analyzed the differences in MCI prevalence among the different variables. The role of sex and age in the association between MCI and HGS was analyzed using binary logistic regression. Results Women had significantly higher prevalence of MCI than men, as did the older group (age ≥70 years) compared with the younger group (age 60–70 years). In men, the low and middle HGS tertiles were significantly associated with MCI. In contrast, only the low tertile of HGS was associated with MCI in women. In the older group, the low tertile of HGS was significantly associated with MCI, which was not observed in the younger group. Conclusions HGS was associated with MCI in older adults, and this association was stronger in men. HGS may be useful for evaluating MCI in older adults.
Courtship feeding in Ospreys Pandion haliaetus: a criterion for mate assessment?

In many bird species males provision their mates prior to egg-laying. Courtship feeding has been suggested to function in several ways: to advance laying date by improving female condition, to induce a female to copulate or to allow a female to assess her mate. The role of courtship feeding in Ospreys Pandion haliaetus was investigated in British Columbia, Canada. Courtship feeding rate affected the probability of a pair initiating a clutch. Pairs that laid eggs had higher rates of courtship feeding than pairs that did not lay eggs in both 1991 and 1992. Male courtship feeding rate also correlated negatively with the duration of the courtship period. Experimentally increasing the amount of food available to females prior to egg-laying resulted in a nonsignificant reduction in the duration of the courtship period. This study found no evidence to support the suggestion that female Ospreys trade copulations for food during the courtship period; only 63 of 385 copulations observed were associated with feeds, and courtship feeding rate did not correlate with the copulation rate of a pair. Male provisioning rates, however, were predictable; courtship feeding rate correlated with both male delivery rate to the nest when chicks were 1–2 weeks old and mean brood growth rate. Female Ospreys therefore may be able to predict the quality of subsequent paternal care using courtship feeding rate. As predicted if optimal hatching asynchrony is dependent on food availability, mean brood growth rate, an indirect measure of male parental care, was negatively correlated with hatching asynchrony. This suggests that female Ospreys may manipulate hatching asynchrony in response to male courtship feeding rate, thereby maximizing the productivity of their brood at predicted food levels.
Antihypertensive drug use and prostate cancer-specific mortality in Finnish men

The aim of this study was to investigate pre- and post-diagnostic use of antihypertensive drugs on prostate cancer (PCa)-specific survival and the initiation of androgen deprivation therapy (ADT). The cohort investigated 8,253 PCa patients with 837 PCa-specific deaths during the median follow-up of 7.6 years after diagnosis. Information on drug use, cancer incidence, clinical features of PCa, and causes of death was collected from Finnish registries. Hazard ratios with 95% confidence intervals were calculated using Cox regression with antihypertensive drug use as a time-dependent variable. Separate analyses were performed on PCa survival related to pre- and post-diagnostic use of drugs and on the initiation of ADT. Antihypertensive drug use overall was associated with an increased risk of PCa-specific death (Pre-PCa: 1.21 (1.04–1.4), Post-PCa: 1.2 (1.02–1.41)). With respect to the separate drug groups, angiotensin II type 1 receptor (ATr) blockers, were associated with improved survival (Post-PCa: 0.81 (0.67–0.99)) and diuretics with an increased risk (Post-PCa: 1.25 (1.05–1.49)). The risk of ADT initiation was slightly higher among antihypertensive drug users as compared to non-users. In conclusion, this study supports anti-cancer effect of ATr blockers on PCa prognosis and this should be investigated further in controlled clinical trials.
Further contribution to cytotaxonomy of the genus Silene L. (Sect. Auriculatae, Caryophyllaceae)

The present study reports the chromosome numbers of 18 Silene L. species subspe- cies and varieties from the sect. Auriculatae for the first time. S. commelinifolia var. isophylla, S. commelinifoilia var. ovatifolia, S. araratica, S. meyeri ssp. persica, S. nizvana, S. oligophylla, S. persica and S. rhynchocarpa showed 2n = 2x = 24 chromosome number, S. pseudoaucheriana, S. gynodioica, S. erysimifolia, S. guntensis, S. goniocaula, S. lucida S. microphylla showed 2n= 4x= 48 and S. hirticalyx had 2n=6x=72 chromosome number. The size of the chromosomes var- ied from 1.53 µm in Ahvan population of S. commelinifolia var. commelinifolia to 4.97 µm in S. oligophylla. The chromosomes were metacentric (m) and sub-metacentric (sm). The species studied differed significantly in total size of the chromosomes, size of the short arms and the long arms indicating the role of quantitative changes of chromosomes in species diversification. The Silene species differed in karyotype formulae and symmetry indicating qualitative changes in the chromosomes possibly due to the occurrence of structural changes. Different clustering and ordination methods showed karyotype distinctness of the species studied.
Comparison of statistical models to estimate daily milk yield in single milking testing schemes

Abstract Different statistical models were compared to estimate daily milk yield from morning or evening milking test results. The experiment was conducted on 14 family farms with 325 recorded cows. The amount of explained variance was higher for models including the effects of partial milk yield, the interval between successive milking, the interaction between partial milk yield and the milking interval and the farm (R2 = 0.976 for AM, R2 = 0.956 for PM) than for models including partial milk yield effect only (R2 = 0.957 for AM, R2 = 0.937 for PM). Estimates of daily milk yield from linear models were more accurate than those obtained by doubling single milking weights. The results show that more complex model gives the best fit to the data. Differences between models according to determination and correlation coefficient were minor. Further investigations on larger sets of data are needed to draw more general conclusion.
Correction for Makary et al., Loss of nucleus accumbens low-frequency fluctuations is a signature of chronic pain

NEUROSCIENCE Correction for “Loss of nucleus accumbens low-frequency fluctuations is a signature of chronic pain,” by Meena M. Makary, Pablo Polosecki, Guillermo A. Cecchi, Ivan E. DeAraujo, Daniel S. Barron, Todd R. Constable, Peter G. Whang, Donna A. Thomas, Hani Mowafi, Dana M. Small, and Paul Geha, which was first published April 20, 2020; 10.1073/pnas.1918682117 (Proc. Natl. Acad. Sci. U.S.A. 117, 10015–10023). The authors note that the disclosure of a competing interest was omitted during publication. The authors declare the following: “P.G. has filed a patent application for the signature of chronic pain described in this article. ” The authors apologize for the oversight. The online version has been corrected. Published under the PNAS license. First published June 29, 2020. www.pnas. org/cgi/doi/10.1073/pnas.2010926117
New Craniodental Remains of the Quaternary Jamaican Monkey Xenothrix mcgregori (Xenotrichini, Callicebinae, Pitheciidae), with a Reconsideration of the Aotus Hypothesis1

Abstract The Jamaican monkey Xenothrix mcgregori is one of several extinct endemic platyrrhines known from the late Quaternary of the Greater Antilles. Until recently, the hypodigm of Xenothrix was limited to the holotype partial mandible and a handful of tentatively referred postcranial elements. Here we describe several additional fossils attributable to Xenothrix, including the first cranial remains, all of which were recovered in cave deposits in the Jackson's Bay region of southern Jamaica. In addition to a partial face from Lloyd's Cave and a maxillary fragment of a different individual from the same site, the craniodental collection includes two incomplete mandibles with poorly preserved cheekteeth from nearby Skeleton Cave. The new specimens confirm a distinctive derived feature of Xenothrix, i.e., reduced dental formula in both jaws (2/2 1/1 3/3 2/2). Although no examples of the maxillary canine are yet known, its alveolus is notably small. Similarly, although the upper face of Xenothrix is also unknown, it is clear that the maxillary sinuses were large enough to encroach significantly on the bases of the zygomatic processes. The nasal fossa is also very large and wider than the palate at the latter's widest point. A similar condition is seen in the extinct Cuban monkey Paralouatta varonai. Xenothrix continues to generate disputes among platyrrhine specialists because its unusual combination of apomorphies complicates its systematic placement. Rosenberger's recent “Aotus hypothesis” stipulates that Xenothrix is a close relative of the living owl monkey (Aotus) and is not a pitheciid sensu stricto. Two fundamental characters used to support this hypothesis—hypertrophied orbits and enlarged central incisors—can be shown to be inapplicable or uninterpretable on the basis of the existing hypodigm of Xenothrix. The new craniodental evidence confirms our earlier cladistic results showing that the Antillean monkeys (Xenothrix mcgregori, Paralouatta varonai, and Antillothrix bernensis) are closely related and that Callicebus is their closest joint extant mainland relative. This may be expressed systematically by placing the three Antillean taxa in Xenotrichini, new tribe, adjacent to Callicebini, their sister-group within subfamily Callicebinae (Pitheciidae).
SILICEOUS SPONGE SPICULES FROM THE MIOCENE MEM MONIZ MARLS (PORTUGAL) AND THEIR ENVIRONMENTAL SIGNIFICANCE

The Miocene (middle Serravalian) Mem Moniz marls from Algarve (Portugal) contain a rich and well preserved assemblage of siliceous sponge spicules, which is described here for the first time. The assemblage indicates that the sponge fauna was dominated by Astrophorida, and in particular by Geodiidae. The presence of Eurylus sp. and probably Geodia sp. (both Astrophorida), Samus sp. (Spirophorida) and Alectona wallichii (Hadromerida) is also reported. Samus sp. and Alectona wallichii are reported from the fossil record for the first time. Additionally, the occurrence of lithistid demosponges (represented by Theonellidae and rhizomorinids), Hadromerida, Spirophorida and Hexactinellida is also shown. Ancorinidae, Pachastrellidae (and/or Cathropellidae), both Astrophorida, were also clearly recognized. Less certain is the occurrence, in the Mem Moniz marls, of Tethyidae (Hadromerida). Bathymetric reconstructions based on sponges are imprecise due to the fact that these organisms often have very wide bathymetric ranges. However, the studied sponge assemblage is clearly neither characteristic of very shallow nor very deep marine environments. The dominance of astrophorids and the presence of lithistids and hexactinellids suggest a depth of at least several tens to one hundred metres, or even more.
Persian Darnel (Lolium persicum) Fecundity Response to Spring Wheat, Canola, and Sunflower Interference1

Persian darnel control options are limited and unmanaged populations can cause substantial crop yield loss. Integrating crop diversification and higher crop seeding rates into a cropping system might improve Persian darnel management. Field experiments were conducted to determine the effect of different crops and increased crop seeding rates on Persian darnel fecundity. Persian darnel produced up to 2,800 seeds per plant and 53,000 seeds/m2 when grown without competition. Increasing crop density reduced Persian darnel tillers per plant, seed weight, and fecundity. Increasing crop density reduced Persian darnel fecundity 0.4 to 0.2% per spring wheat plant, 0.6 to 0.1% per canola plant, and 16 to 8% per sunflower plant. Persian darnel fecundity was impacted the greatest by reduced weed seedling establishment, which was caused by crop competition and seeding sunflower late in the spring preceded by a nonselective herbicide application. Results indicated delaying the seeding of spring crops or including a late-seeded warm season crop, like sunflower or safflower, in the cropping system is an effective weed management tool for reducing Persian darnel fecundity. Nomenclature: Glyphosate; Persian darnel, Lolium persicum Boiss. & Hoh. #3 LOLPS; canola, Brassica napus Koch. ; spring wheat, Triticum aestivum L. ; sunflower, Helianthus annuus L. Additional index words: Fecundity, preplant herbicide, seedling establishment, seeding date, seeding rate, stale seedbed, weed interference, yield components.
Plant Growth Enhancement using Rhizospheric Halotolerant Phosphate Solubilizing Bacterium Bacillus licheniformis QA1 and Enterobacter asburiae QF11 Isolated from Chenopodium quinoa Willd

Plant growth-promoting rhizobacteria represent a promising solution to enhancing agricultural productivity. Here, we screened phosphate solubilizing bacteria from the rhizospheric soil of Chenopodium quinoa Willd and assessed their plant-growth promoting rhizobacteria (PGPR) properties including production of indole-3-acetic acid (IAA), siderophores, hydrogen cyanide (HCN), ammonia and extracellular enzymes. We also investigated their tolerance to salt stress and their capacity to form biofilms. Two isolated strains, named QA1 and QF11, solubilized phosphate up to 346 mg/L, produced IAA up to 795.31 µg/mL, and tolerated up to 2 M NaCl in vitro. 16S rRNA and Cpn60 gene sequencing revealed that QA1 and QF11 belong to the genus Bacillus licheniformis and Enterobacter asburiae, respectively. In vivo, early plant growth potential showed that quinoa seeds inoculated either with QA1 or QF11 displayed higher germination rates and increased seedling growth. Under saline irrigation conditions, QA1 enhanced plant development/growth. Inoculation with QA1 increased leaf chlorophyll content index, enhanced P and K+ uptake and decreased plant Na+ uptake. Likewise, plants inoculated with QF11 strain accumulated more K+ and had reduced Na+ content. Collectively, our findings support the use of QA1 and QF11 as potential biofertilizers.
Aneuploid Circulating Tumor-Derived Endothelial Cell (CTEC): A Novel Versatile Player in Tumor Neovascularization and Cancer Metastasis

Hematogenous and lymphogenous cancer metastases are significantly impacted by tumor neovascularization, which predominantly consists of blood vessel-relevant angiogenesis, vasculogenesis, vasculogenic mimicry, and lymphatic vessel-related lymphangiogenesis. Among the endothelial cells that make up the lining of tumor vasculature, a majority of them are tumor-derived endothelial cells (TECs), exhibiting cytogenetic abnormalities of aneuploid chromosomes. Aneuploid TECs are generated from “cancerization of stromal endothelial cells” and “endothelialization of carcinoma cells” in the hypoxic tumor microenvironment. Both processes crucially engage the hypoxia-triggered epithelial-to-mesenchymal transition (EMT) and endothelial-to-mesenchymal transition (EndoMT). Compared to the cancerization process, endothelialization of cancer cells, which comprises the fusion of tumor cells with endothelial cells and transdifferentiation of cancer cells into TECs, is the dominant pathway. Tumor-derived endothelial cells, possessing the dual properties of cancerous malignancy and endothelial vascularization ability, are thus the endothelialized cancer cells. Circulating tumor-derived endothelial cells (CTECs) are TECs shed into the peripheral circulation. Aneuploid CD31+ CTECs, together with their counterpart CD31- circulating tumor cells (CTCs), constitute a unique pair of cellular circulating tumor biomarkers. This review discusses a proposed cascaded framework that focuses on the origins of TECs and CTECs in the hypoxic tumor microenvironment and their clinical implications for tumorigenesis, neovascularization, disease progression, and cancer metastasis. Aneuploid CTECs, harboring hybridized properties of malignancy, vascularization and motility, may serve as a unique target for developing a novel metastasis blockade cancer therapy.
Effect of computer-mediated communication competency on young adults’ personal development: The mediating roles of online engagement

This study was conducted to investigate the effects of computer-mediated communication competency (self-efficacy, motivation and knowledge) on young adults’ personal development (i.e. self-esteem, satisfaction with university life and acceptance). In addition, the study examined whether young adults’ online engagement mediates the relationships between components in the computer-mediated communication competency and personal development. A survey was administered in three public universities where young adults were found to be heavily engaged online. A total of 600 questionnaires were distributed and a total of 548 questionnaires were returned, cleaned and used in the analysis. The study found several relationships: i) Motivation affects the young adults’ self-esteem, satisfaction with university life and acceptance; ii) Knowledge affects self-esteem and satisfaction with university life: iii) Self-efficacy only affects satisfaction with university life. However, online engagement was found to mediate motivation with acceptance as well as knowledge with acceptance. The implications of the findings are also discussed.
Visual Morbidity in Ocular Tuberculosis – Collaborative Ocular Tuberculosis Study (COTS)-1: Report #6

ABSTRACT Objective: Aim of the study was to examine extent, natural history, and clinical features associated with visual impairment (VI) in patients diagnosed with ocular tuberculosis (OTB) by the Collaborative Ocular Tuberculosis Study (COTS)-1. Methods: Multi-center retrospective cohort study. Main outcomes were VI. Results: A total of 302 patients were included in the study, including 175 patients whose data related to BCVA were available throughout the 2 years of follow up. Mean BCVA grossly improved at 12, 18, and 24 months of follow-up (p < .001). Mean BCVA was worse at 12–18th month follow-up for patients treated with ATT versus patients who were not treated with ATT, but patients treated with ATT had a statistically significant improvement in BCVA at the 24-month endpoint. Conclusions: OTB is associated with significant visual morbidity, future well-designed prospective studies are warranted to establish the causal association between OTB and visual loss.
Genetics of Apical Dominance in Plantain (Musa spp., AAB Group) and Improvement of Suckering Behavior

Apical dominance, i.e., the inhibition of lateral bud growth due to growth substances released by the terminal bud, has been considered as a limiting factor for the perennial productivity of plantains ( Musa spp., AAB group). Segregation ratios in F 1 and F 2 plantain-banana hybrids suggest that inheritance of apical dominance is controlled by a major recessive gene, ad. The dominant Ad allele improved the suckering of plantain-banana hybrids, as measured by the height of the tallest sucker at flowering and harvest. At harvest, the ratoon crop of the diploid and tetraploid hybrids had completed 70% to 100% of its vegetative development, whereas the ratoon of the plantain parents, due to high apical dominance, was only at 50% of total pseudostem growth. Sucker growth rates are generally the result of gibberellic acid (GA 3 ) levels, and it is suggested that the Ad gene regulates GA 3 production. However, the Ad gene has incomplete penetrance, genetic specificity, and variable expressivity. Increased frequency of the Ad gene and a commensurate improvement in the suckering behavior of the diploid populations may be achieved by phenotypic recurrent selection. Plantain and banana (Musa spp.) are important food crops in the humid forest and mid-altitude agroecologies of sub-Saharan Af- rica. They are high-yielding and form an integral component of the farming systems in these ecologies. In addition to being a staple food for rural and urban consumers, plantain and banana provide an important source of rural income. The crop is mainly produced by smallholders in compound or home gardens as well as in large fields (Swennen, 1990; Swennen and Vuylsteke, 1991). Cultivated Musa are mostly triploids (2n = 3x = 33). Being almost completely sterile, they develop fruit by parthenocarpy. The most important cultivars vary in their genomic constitution and are generally classified as follows: dessert bananas (AAA), East African highland bananas (AAA), plantains (AAB), and starchy bananas. The genome of the cultivated types is derived from the diploid wild species M. acuminata Colla and M. balbisiana Colla, which contributed the A and B genomes, respectively (Simmonds, 1966). Different types are cultivated in distinct ecoregions. Thus, the AAB plantains are predominant in the humid lowlands of West and Central Africa, while AAA cooking and beer bananas prevail in the East African highlands (Vuylsteke et al.,