Miracle-dz/UniFAR-FTUs huggingface dataset:
Title: Use of finger length ratio as a marker for knee osteoarthritis: A case-control study of 2,456 patients Running/Short Title: Can finger lengths be used as a marker for knee osteoarthritis? Article category: Qualitative research

Background: In the human hand, the index and ring finger present a considerable variation in their relative lengths and the ratio of their lengths (2D:4D ratio). This ratio is associated with a variety of behavioral and physiological traits possibly linked to variation in sex hormones levels. Previous studies have revealed inconsistent results while assessing the association of 2D:4D ratio as a risk factor for occurrence of knee osteoarthritis (KOA). This study was designed as a prospective observational study to analyze this association using a better methodology. Methods: Patients were enrolled into KOA group (1396 patients) and non-KOA group (1060 patients) based on ACR criteria for OA knee. Knee and hand radiographs of all patients enrolled were assessed. The 2D:4D length ratio was calculated for phalanges, metacarpal bones and for the combined (metacarpal & phalanx) finger lengths on radiographs and visual finger lengths. The finger patterns were classified and assessment was done between these ratios and finger pattern types for occurrence and severity of KOA. Results: A lower 2D:4D ratio in an individual was associated with an increased chance of KOA and a dose response relationship was found between radiographic grading of KOA and 2D:4D . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted July 24, 2020. ; https://doi.org/10.1101/2020.07. 22.20159681 doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. ratio. Conclusion: Based on the findings of this study one can predict the risk of developing KOA using this simple technique which can be used as a screening tool whereby preventive intervention can be started if someone presents early with a low 2D:4D finger length ratio.
Karyological characterization of a new population of Akodon lindberghi (Rodentia, Sigmodontinae) in Minas Gerais State (Brazil)

SUMMARYThe G-band karyotype of Akodon lindberghi (2n = 42, FN = 42) has been described in eight wild caught specimens captured outside its type locality, C-banding showed distinct heterochromatic regions at the centromere of all chromosomes. Ag-NOR staining showed a maximum of 12 NORs per cell per individual with a mean number of 1.4 per metaphase.
Childhood hypopituitarism: Etiological pattern in a major teaching hospital in Saudi Arabia.

Background: Childhood hypopituitarism is a clinical syndrome of deficiency in pituitary hormone production. It might be partial or complete. Presentation varies from asymptomatic to acute collapse depending on the etiology, rapidity of onset, and predominant hormone involved. Design and setting: A retrospective hospital based study was conducted at the pediatric endocrine service, King Khalid University Hospital (KKUH) Riyadh, Saudi Arabia during the period of January 1989 and December 2017. Material and methods: The medical records of patients with the diagnosis of hypopituitarism were retrospectively reviewed. Data included age, sex, clinical presentation, and results of relevant laboratory investigations and radiological imaging. Results: During the period under review, a total of 202 patients were diagnosed to have hypopituitarism. Mean age at diagnosis was 8.9 years, range 0-18 years. A brain MRI was helpful in identifying the cause. A diversity of causes was encountered with a non-tumor causes being the commonest. Conclusion: Childhood hypopituitarism is not that rare. A brain MRI scan is critical in attempting to determine the specific cause and plan the management.
Effects of seedling age and size on chloride accumulation by juvenile citrus seedlings treated with sodium chloride under glasshouse conditions

Chloride accumulation by juvenile citrus seedlings treated with sodium chloride for 56 days, using either nutrient solution culture (50 mM NaCl) or pot culture (75 mM NaCl) techniques under glasshouse conditions, was investigated in relation to seedling age. Ranking of cultivars on the basis of leaf chloride concentrations varied according to the age of seedlings examined. Leaf chloride concentrations of 6-, 5-, 4- and 3-month-old seedlings of eight cultivars examined in solution culture decreased with seedling age and were negatively correlated with seedling dry weight within some cultivars. Cultivar differences in leaf chloride concentrations, which occurred for all age groups, were negatively correlated with shoot growth and seedling dry weight for 5-month-old seedlings only. Leaf chloride concentrations of seedlings treated with NaCl in pot culture also changed with the age of seedlings (5, 17- and 29-monthsold) and varied between cultivars, with significant cultivar x age interactions. The effect of seedling size on chloride accumulation was investigated using nutrient solution culture. Six-month-old seedlings of four varieties were treated with NaCl (50 mM) for 56 days. Two size classes were obtained by growing seedlings at two densities before salt treatment. Small seedlings had greater shoot chloride concentrations than equivalent large seedlings and cultivar ranking, based on shoot chloride concentrations, changed with seedling size. Cultivar differences in leaf chloride concentrations were negatively correlated with seedling growth and dry weight for small seedlings but not for large seedlings. Seedling size had no effect on root chloride concentrations. The results suggest that screening very small seedlings for chloride exclusion is not feasible since rankings based on leaf chloride concentrations did not agree with documented data for grafted trees. There appeared to be a critical or threshold seedling age or size at or above which rankings for shoot chloride accumulation by good chloride excluders were consistent with documented field data. The results are discussed in relation to screening citrus hybrids for chloride exclusion under glasshouse conditions.
INCORPORATING AVAILABILITY FOR DETECTION IN ESTIMATES OF BIRD ABUNDANCE

Abstract Several bird-survey methods have been proposed that provide an estimated detection probability so that bird-count statistics can be used to estimate bird abundance. However, some of these estimators adjust counts of birds observed by the probability that a bird is detected and assume that all birds are available to be detected at the time of the survey. We marked male Henslow's Sparrows (Ammodramus henslowii) and Grasshopper Sparrows (A. savannarum) and monitored their behavior during May-July 2002 and 2003 to estimate the proportion of time they were available for detection. We found that the availability of Henslow's Sparrows declined in late June to <10% for 5- or 10-min point counts when a male had to sing and be visible to the observer; but during 20 May-19 June, males were available for detection 39.1% (SD = 27.3) of the time for 5-min point counts and 43.9% (SD = 28.9) of the time for 10-min point counts (n = 54). We detected no temporal changes in availability for Grasshopper Sparrows, but estimated availability to be much lower for 5-min point counts (10.3%, SD = 12.2) than for 10-min point counts (19.2%, SD = 22.3) when males had to be visible and sing during the sampling period (n = 80). For distance sampling, we estimated the availability of Henslow's Sparrows to be 44.2% (SD = 29.0) and the availability of Grasshopper Sparrows to be 20.6% (SD = 23.5). We show how our estimates of availability can be incorporated in the abundance and variance estimators for distance sampling and modify the abundance and variance estimators for the double-observer method. Methods that directly estimate availability from bird counts but also incorporate detection probabilities need further development and will be important for obtaining unbiased estimates of abundance for these species. Incorporación de la Disponibilidad para la Detección en las Estimaciones de Abundancia de Aves
Additional microsatellites for Sparus aurata and cross-species amplification within the Sparidae family

Six new microsatellite loci were isolated and characterized in 32 individuals from a farm population of gilthead seabream (Sparus aurata). Expected heterozygosity at all loci was high, ranging from 0.835 to 0.958 with between 10 and 27 alleles per locus. A multiplex polymerase chain reaction protocol was developed using four of the loci. Cross-species amplification of the loci was tested in six species of the Sparidae family and four loci were successfully amplified in two or more related species.
Complexity of Two-dimensional Bootstrap Percolation Difficulty: Algorithm and NP-Hardness

Bootstrap percolation is a class of cellular automata with random initial state. Two-dimensional bootstrap percolation models have three rough universality classes, the most studied being the `critical' one. For this class the scaling of the quantity of greatest interest -- the critical probability -- was determined by Bollobas, Duminil-Copin, Morris and Smith in terms of a simply defined combinatorial quantity called `difficulty', so the subject seemed closed up to finding sharper results. However, the computation of the difficulty, was never considered. In this paper we provide the first algorithm to determine this quantity, which is, surprisingly, not as easy as the definition leads to thinking. The proof also provides some explicit upper bounds, which are of use for bootstrap percolation. On the other hand, we also prove the negative result that computing the difficulty of a critical model is NP-hard. This two-dimensional picture contrasts with an upcoming result of Balister, Bollobas, Morris and Smith on uncomputability in higher dimensions. The proof of NP-hardness is achieved by a technical reduction to the Set Cover problem.
No Correlation between Latewood Formation and Leader Growth in Douglas-Fir Saplings

SUMMARY The width of earlywood and latewood in conifer xylem may have a profound effect on water transport and storage, vulnerability to embolism, and wood strength, yet the controls over the timing of latewood formation are unclear. Tracheids differentiating in the cambial zone are influenced by IAA indole-3 acetic acid, the radial concentration gradient of which appears to either increase cell expansion (earlywood) or increase cell wall deposition (latewood). There are suggestive data that latewood begins to form when the growth of the leader stops, but defini tive results are lacking. Height growth was measured in 14 Douglas-fir (Pseudotsuga menziesii) saplings at 10 dates between May and August, from the beginning of the growing season until after height growth had ceased. The cambium was also pinned six times between June and July, to induce xylem scarring at known dates. After height growth ceased, saplings were harvested and transverse sections of the wood were made at the pin insertion points. The date at which 95% of the height growth had occurred and the date at which latewood formation had begun were estimated. Analysis showed no correlation of these data, suggesting that the two phenomena may occur around the same time, but that one is not causal of the other.
The consequences of differential family survival rates and equalizing maternal contributions on the effective population size (Ne) of cultured silver‐lipped pearl oysters, Pinctada maxima

The effective population size (Ne) is a critical gauge of how efficiently an aquaculture operation is capturing or maintaining genetic diversity and can govern the long-term success of genetic selection programmes. In communally reared pearl oysters (Pinctada maxima), high variance in family sizes is a significant contributor towards low Ne and its severity may be compounded by differential survival rates of individual families. To determine the effect of variable survival on Ne in cultured P. maxima, families from two commercial populations were analysed using DNA parentage analyses to monitor survival and changes in relative contributions. Significant shifts in relative contributions were observed between 72 days and 18 months of age in both commercial cohorts (P<0.001). Survival rates were found to be highly variable among families (ranging from 2.5% to 49.5%) when reared in a common environment. Additionally, we investigated whether equalizing maternal family sizes before communal rearing will reduce family size variance, and increase Ne, compared with stocking at naturally produced proportions. Family equalization (E) significantly improved Ne (P50.013) compared with rearing at natural (N) proportions (E: Ne = 7.18 +- 0.34; N: Ne = 5.60 +- 0.15); however, this practice may unintentionally magnify negative influences of poor performing families if survival is correlated with other commercially important traits. It is concluded that highly variable family survival will affect Ne in communally reared P. maxima, and the practice of equalizing family sizes in order to maximize Ne may only become consistently beneficial once further progress is made towards understanding, and then reducing variation in family survival rates.
Are Tart Cherry Supplements Effective on Reducing Muscle Soreness and Perception of Pain in Young, Healthy Males Following High Intensity Resistance Training?

OBJECTIVE: The objective of this selective EBM review is to determine whether or not tart cherry supplements are effective at alleviating muscle soreness and pain following high resistance training. STUDY DESIGN: Review of two double blind randomized control trials, and one crossover randomized control trial. All three studies were published in English between 2006-2015. DATA SOURCES: Two double blind randomized control trials and one crossover randomized control trial found using Cochrane and PubMed. OUTCOMES MEASURED: The outcomes measured were muscle soreness and perception of pain. They were measured using a pressure-pain threshold and 10 point pain scale RESULTS: The first study, the Bowtell study showed tart cherry may provide a small amount of relief as assessed through pressure-pain threshold, but has not proven in this study to be statistically significant. The second study, the Connolly study indicate tart cherry supplements significantly aid in subjective measures of pain but not tenderness. The third study, the Levers study revealed overall, the tart cherry supplement significantly decreased participants perception of muscle soreness. No serious adverse events were noted in any of the three studies. CONCLUSIONS: Based on these three trials, it is inconclusive whether tart cherry supplements are an effective treatment for musculoskeletal pain and soreness following high intensity resistance training. Not all results were statistically significant; however, each study showed some improvement in muscle soreness and perception of pain. Therefore, though more research is needed, tart cherry supplements may provide an alternative to or supplement to the use of nonsteroidal anti-inflammatories.
Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method

Improvements in sequencing technology continue to drive sequencing cost towards $100 per genome. However, mapping sequenced data to a reference genome remains a computationally-intensive task due to the dependence on edit distance for dealing with INDELs and mismatches introduced by sequencing. All modern aligners use seed–filter–extend methodology and rely on filtration heuristics to reduce the overhead of edit distance computation. However, filtering has inherent performance–accuracy trade-offs that limits its effectiveness. Motivated by algorithmic advances in randomized low-distortion embedding, we introduce SEE, a new methodology for developing sequence mappers and aligners. While SFE focuses on eliminating sub-optimal candidates, SEE focuses instead on identifying optimal candidates. To do so, SEE transforms the read and reference strings from edit distance regime to the Hamming regime by embedding them using a randomized algorithm, and uses Hamming distance over the embedded set to identify optimal candidates. To show that SEE performs well in practice, we present Accel-Align an SEE-based short-read sequence mapper and aligner that is 3–12×\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document} faster than state-of-the-art aligners on commodity CPUs, without any special-purpose hardware, while providing comparable accuracy. As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be achieved by using edit distance. Thus, the techniques presented in this paper have a much broader scope as they can be used for other applications like graph alignment, multiple sequence alignment, and sequence assembly.
Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic

The worldwide eruption of COVID-19 that began in Wuhan, China in late 2019 reached 10 million cases by late June 2020. In order to understand the epidemiological landscape of the COVID-19 pandemic, many studies have attempted to elucidate phylogenetic relationships between collected viral genome sequences using haplotype networks. However, currently available applications for network visualization are not suited to understand the COVID-19 epidemic spatiotemporally, due to functional limitations That motivated us to develop Haplotype Explorer, an intuitive tool for visualizing and exploring haplotype networks. Haplotype Explorer enables people to dissect epidemiological consequences via interactive node filters to provide spatiotemporal perspectives on multimodal spectra of infectious diseases, including introduction, outbreak, expansion, and containment, for given regions and time spans. Here, we demonstrate the effectiveness of Haplotype Explorer by showing an example of its visualization and features. The demo using SARS-CoV-2 genome sequences is available at https://github.com/TKSjp/HaplotypeExplorer Summary A lot of software for network visualization are available, but existing software have not been optimized to infection cluster visualization against the current worldwide invasion of COVID-19 started since 2019. To reach the spatiotemporal understanding of its epidemics, we developed Haplotype Explorer. It is superior to other applications in the point of generating HTML distribution files with metadata searches which interactively reflects GISAID IDs, locations, and collection dates. Here, we introduce the features and products of Haplotype Explorer, demonstrating the time-dependent snapshots of haplotype networks inferred from total of 4,282 SARS-CoV-2 genomes.
Molecular evidence for cosmopolitan distribution of platyhelminth parasites of tunas (Thunnus spp.)

Global distribution of platyhelminth parasites and their host specificities are not well known. Our hypothesis was that platyhelminth parasites of large pelagic fishes are common around the world. We analysed molecular variation in three different taxa of platyhelminth parasites infecting four species of tunas: yellowfin tuna (Thunnus albacares, Scombridae) from Western Australia, southern bluefin tuna (Thunnus maccoyii, Scombridae) from South Australia, Pacific bluefin tuna (Thunnus orientalis, Scombridae) from Pacific Mexico and northern bluefin tuna (T. thynnus, Scombridae) from two localities in the Mediterranean (Spain and Croatia). Comparisons of ITS2 and partial 28S rDNA demonstrated two congeneric species of blood flukes (Digenea: Sanguinicolidae) from multiple hosts and localities: Cardicola forsteri from southern bluefin and northern bluefin tunas, and Cardicola sp. from Pacific bluefin and northern bluefin tunas; and a gill fluke, Hexostoma thynni (Polyopisthocotylea: Hexostomatidae), from yellowfin, southern bluefin and northern bluefin tunas. Partial 28S rDNA indicates that a second type of fluke on the gills, Capsala sp. (Monopisthocotylea: Capsalidae), occurs on both southern bluefin and Pacific bluefin tunas. This appears to be the first report of conspecific platyhelminth parasites of teleosts with a wide-ranging geographical distribution that has been confirmed through molecular approaches. Given the brevity of the free-living larval stage of both taxa of flukes on the gills (H. thynni and Capsala sp.), we conclude that the only feasible hypothesis for the cosmopolitan distribution of these flatworms is migrations of host tunas. Host migration also seems likely to be responsible for the widespread occurrence of the two species of blood flukes (Cardicola spp.), although it is also possible that these were translocated recently by the spread of infected intermediate hosts.
Ase1 domains dynamically slow anaphase spindle elongation and recruit Bim1 to the midzone

How cells regulate microtubule crosslinking activity to control the rate and duration of spindle elongation during anaphase is poorly understood. In this study, we test the hypothesis that PRC1/Ase1 proteins use distinct microtubule-binding domains to control spindle elongation rate. Using budding-yeast Ase1, we identify unique contributions for the spectrin and carboxy-terminal domains during different phases of spindle elongation. We show that the spectrin domain uses conserved, basic residues to promote the recruitment of Ase1 to the midzone before anaphase onset and slow spindle elongation during early anaphase. In contrast, a partial Ase1 carboxy-terminal truncation fails to form a stable midzone in late anaphase, produces faster elongation rates after early anaphase, and exhibits frequent spindle collapses. We find that the carboxy-terminal domain interacts with the plus-end tracking protein EB1/Bim1 and recruits Bim1 to the midzone to maintain midzone length. Overall, our results suggest that the Ase1 domains provide cells with a modular system to tune midzone activity and control elongation rates.
Integration of Transcriptome and Small RNA Sequencing to Decipher Molecular Interaction of Chenopodium quinoa Varieties with Cucumber Mosaic Virus

Saponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa to Cucumber mosaic virus (CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties × +/- CMV × 1 or 4 days after inoculation × 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In ‘Red Head’, (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.