Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of automated and manual quantification methods for neuromelanin‐sensitive MRI in Parkinson's disease

Neuromelanin‐sensitive magnetic resonance imaging quantitative analysis methods have provided promising biomarkers that can noninvasively quantify degeneration of the substantia nigra in patients with Parkinson's disease. However, there is a need to systematically evaluate the performance of manual and automated quantification approaches. We evaluate whether spatial, signal‐intensity, or subject specific abnormality measures using either atlas based or manually traced identification of the substantia nigra better differentiate patients with Parkinson's disease from healthy controls using logistic regression models and receiver operating characteristics. Inference was performed using bootstrap analyses to calculate 95% confidence interval bounds. Pairwise comparisons were performed by generating 10,000 permutations, refitting the models, and calculating a paired difference between metrics. Thirty‐one patients with Parkinson's disease and 22 healthy controls were included in the analyses. Signal intensity measures significantly outperformed spatial and subject specific abnormality measures, with the top performers exhibiting excellent ability to differentiate patients with Parkinson's disease and healthy controls (balanced accuracy = 0.89; area under the curve = 0.81; sensitivity =0.86; and specificity = 0.83). Atlas identified substantia nigra metrics performed significantly better than manual tracing metrics. These results provide clear support for the use of automated signal intensity metrics and additional recommendations. Future work is necessary to evaluate whether the same metrics can best differentiate atypical parkinsonism, perform similarly in de novo and mid‐stage cohorts, and serve as longitudinal monitoring biomarkers.
Structure and metamorphism beneath the obducting Oman ophiolite: Evidence from the Bani Hamid granulites, northern Oman mountains

The Cretaceous Semail ophiolite (northern Oman and the United Arab Emirates) includes an intact thrust slice of Tethyan oceanic crust and upper mantle formed above a northeast-dipping subduction zone that was the site of initiation of obduction. The normal metamorphic sole of the Semail ophiolite comprises a highly condensed sequence of hornblende + plagioclase ± garnet amphibolites with small enclaves of garnet + clinopyroxene granulites immediately beneath the mantle sequence peridotites, tectonically underlain by a series of epidote amphibolite and greenschist facies lithologies in a highly deformed ductile shear zone. Peak metamorphic conditions of 770–900 °C and 11–15 kbar indicate metamorphism at depths far greater than can be accounted for by the preserved thickness of the ophiolite (∼15 km). In the mountains of northern Oman, the 1.2-km-thick Bani Hamid thrust sheet is composed of intensely folded granulite and amphibolite facies rocks within mantle sequence peridotites, exhumed by late-stage out-of-sequence thrusting along the Bani Hamid thrust. The Bani Hamid thrust slice includes two-pyroxene quartzites (± hornblende, cordierite, sapphirine), diopside + andradite garnet + wollastonite + scapolite marbles and calc-silicates and amphibolites (hornblende + plagioclase ± clinopyroxene ± biotite) with localized partial melting, intruded by hornblende pegmatites. The Bani Hamid granulites represent metamorphosed cherts and calcareous turbidites probably derived from the distal Haybi Complex and Oman Exotic limestones, which have an alkali basaltic substrate. Metamorphic modeling using the program THERMOCALC in the system NCKFMASHTO (Na 2 O-CaO-K 2 O-FeO-MgO-Al 2 O 3 -SiO 2 -H 2 O-TiO 2 -O) gives peak pressure-temperature conditions of 850 ± 60 °C and 6.3 ± 0.5 kbar, a pressure that is much lower than that of the metamorphic sole, suggesting a different origin. The 206 Pb/ 238 U zircon dates indicate that the gabbroic crust of the ophiolite formed by ridge magmatism from before 96.1 to 95.5 Ma. The 206 Pb/ 238 U zircon dates from the metamorphic sole range from 95.7 to 94.5 Ma, and suggest that metamorphism and melting was either synchronous with or slightly postdated ridge magmatism. The Bani Hamid granulites are younger; zircon and titanite U-Pb dates span ca. 94.5–89.8 Ma. Peraluminous granitic dikes intruding the mantle sequence peridotites are as young as 91.4 Ma and likely reflect localized partial melting of crustal material during the late stage of the obduction process. A minimum of 130 km shortening is recorded by restoration of the major folds within the Bani Hamid thrust sheet, and more than 30 km offset has occurred along the west-directed breaching out-of-sequence Bani Hamid thrust. These rocks may be representative of deep-level duplexes imaged on recent seismic sections across the mountains of northern Oman–United Arab Emirates.
The effect of plant spacing on the yield and bolting of two cultivars of overwintered bulb onions

SummaryThe total and ware bulb yields of both an early-and a late-maturing cultivar of overwintered onion increased linearly with increasing plant densities between 43 and 129 plants m-2. A rectangularity of 1.0 (square arrangement) gave yields 15 to 20% higher than a rectangularity of 8.0 over the range of densities studied. Sowings made in mid-or late-August gave the highest bulb yields whereas early August sowings resulted in a high proportion of plants bolting (flowering) rather than bulbing. The cultivars differed markedly in their susceptibility to bolting but the proportion of plants bolting was not affected by spacing. An equation with two fitted constants relating bulb yield to plant density and the proportion of plants bolting accounted for 82% of the variation. The variability of bulb weight was significantly greater in the later maturing cultivar which was open pollinated than in the earlier cultivar which was a hybrid.
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins

Age is necessary information for the study of life history of wild animals. A general method to estimate the age of odontocetes is counting dental growth layer groups (GLGs). However, this method is highly invasive as it requires the capture and handling of individuals to collect their teeth. Recently, the development of DNA‐based age estimation methods has been actively studied as an alternative to such invasive methods, of which many have relied on used biopsy samples. However, if DNA‐based age estimation can be developed from faecal samples, age estimation can be performed entirely non‐invasively. We developed an age estimation model using the methylation rate of two gene regions, GRIA2 and CDKN2A, measured through methylation‐sensitive high‐resolution melting (MS‐HRM) from faecal samples of wild Indo‐Pacific bottlenose dolphins (Tursiops aduncus). The age of individuals was known through conducting longitudinal individual identification surveys underwater. Methylation rates were quantified from 36 samples collected from 30 individuals. Both gene regions showed a significant correlation between age and methylation rate. The age estimation model was constructed based on the methylation rates of both genes which achieved sufficient accuracy (after LOOCV: MAE = 5.08, R2 = 0.33) for the ecological studies of the Indo‐Pacific bottlenose dolphins, with a lifespan of 40–50 years. This is the first study to report the use of non‐invasive faecal samples to estimate the age of marine mammals.
Resilience in Iranian adolescents during the COVID-19 pandemic: Psychometric Evaluation of the Connor-Davidson Resilience Scale

Background: Resilience is a measure of the ability to cope with stress and the accurate measurement of it is critical. This study aimed to translate and evaluate the psychometric properties of the Connor-Davidson Resilience Scale in Iranian adolescents during the Coronavirus Disease (COVID-19) pandemic. Methods: In this cross-sectional study, after the scale translation, the content and construct validity were assessed using exploratory and confirmatory factor analysis. Moreover, internal consistency, composite reliability, and invariance measurement were evaluated. Results: The content validity ratio was greater than 0.49, and the modified kappa coefficient for all items was higher than 0.6. With exploratory factor analysis, two factors were extracted consisting of 16 items and explaining 43% of the total variance. The results of confirmatory factor analysis indicated a good fit for the model. Cronbach’s alpha and composite reliability for both factors were greater than 0.7. Although there is no significant difference (p = 0.09) in the average resilience of adolescents in different provinces, boys (42.64 ± 10.90) had a significantly (p < 0.001) higher resilience score than girls (40.10 ± 11.92). Conclusion: The study results showed that the Persian 16-item version of the Connor-Davidson Resilience Scale has acceptable reliability and validity in the Iranian adolescent population.
A Hitchhiker's guide to RNA–RNA structure and interaction prediction tools

Abstract RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA–RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA–RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA–RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
A 1437-year Precipitation History From Qilian Juniper in the Northeastern Qinghai-Tibetan Plateau

preceded the Mid-Pleistocene revolution at 0.9 myr when the boreal ice sheet increased in size and the prevailing glacial cyclicity changed from ~40 kyr to ~100kyr. Before the Quaternary, δ13Cmax usually occurred at times of minimal eccentricity forcing, and the long term-variations in δ13C and δ18O display the same 400 kyr cycles; but in the Quaternary, δ13Cmax-II and δ13Cmax-III are out of phase with this astronomical cycle (Fig.1). Therefore, prior to the formation of large ice sheets in the Northern Hemisphere, δ13C co-varied with δ18O in the ocean records but in Quaternary times the 400-kyr cyclicity waned in the δ18O records and apparently “stretched” into 500 kyr in δ13C. The origin of the δ13Cmax episodes in the Quaternary and the nature of the long-term cycles remain unclear. Our working hypothesis suggests that the long-term cycles in weathering intensity in tropical areas may give rise to increased fl ux of Si from land to ocean, which may change the diatom/coccolith ratio in phytoplankton and subsequently the organic/inorganic carbon ratio in sediments. There is strong evidence for the 400-kyr cyclicity in monsoon climate and in opal production in the ocean that is well-correlated with the δ13C record. However, more work is needed to fi nd out the mechanism behind the observed changes in carbon cycling. A common practice in Quaternary climate history studies is just to peruse ice-volume variations as exhibited by δ18O, by considering carbon system changes as the consequences of ice-volume changes. The new discovery shows that long-term changes in carbon reservoirs on the Earth have their own periodicity and their own history, and do not simply follow ice cap variations in the Northern Hemisphere. The Quaternary period has passed through three major stages defi ned by four δ13Cmax events, and each appears to represent a further step in icecap development. Now the Earth is passing through a new carbon isotope maximum, δ13Cmax-I. It is therefore crucial to understand the physical and climatic signifi cance of the long-term carbon cycles, if we are to predict the natural long-term changes of global climate.
Perspectives of Older Adults on COVID-19 and Influenza Vaccination in Ontario, Canada

Introduction/Objectives: Addressing vaccine hesitancy has become an increasingly important public health priority in recent years. There is a paucity of studies that have focused on vaccine hesitancy among older adults, who are known to be at greater risk of complications from infections such as COVID-19. We aim to explore the attitudes and beliefs of older adults regarding COVID-19 and influenza vaccines in Toronto, Ontario. Methods: Older adults enrolled in the Student Senior Isolation Prevention Partnership (SSIPP) program at the University of Toronto were contacted to participate in a phone survey and semi-structured interview. Survey data was analyzed descriptively, and attitude toward vaccination was compared between sociodemographic groups by using Fisher’s exact test. Interview audio files were transcribed verbatim and analyzed inductively for themes and sub-themes. Results: All thirty-three (100%) older adults reported that they had received the first and second doses of the COVID-19 vaccine. Twenty-six (78.8%) participants reported intent to get vaccinated against influenza or had already received the influenza vaccine that year. Notably, only 2 out 7 (28.6%) individuals who did not plan to get vaccinated against influenza believed that vaccines offered by health providers are beneficial and only 3 out of 7 (42.9%) agreed that getting vaccines is a good way to protect oneself from disease. No other significant differences in attitudes among participants were found when compared by gender, ethnicity, or education level. The qualitative data analysis of interview transcripts identified 5 themes that impact vaccine decision making: safety, trust, mistrust, healthcare experience, and information dissemination and education. Conclusions: Our data showed that older adults in the SSIPP program generally had positive views toward vaccination, especially toward the COVID-19 vaccines. However, several concerns regarding the effectiveness of the vaccines were brought up in interviews, such as the speed at which the vaccines were produced and the inconsistency in government messaging.
A growth model for sugar-cane based on a simple carbon balance and the CERES· Maize water balance

The economic optimum harvest age for sugar-cane depends to a large extent on how rates of photosynthesis and respiration change with age. A simple model of the carbon balance in which a constant photosynthetic efficiency was assumed, accounted to a large extent for dry matter accumulation by cv. NCo376 grown under irrigation. Rain-fed crops of this cultivar were simulated by linking the model of the carbon balance to the CERES-Maize water balance routine. The combined model was validated with data from a comprehensive growth analysis experiment undertaken by staff of the SASA Experiment Station in the 1960's. Dry matter accumulation was explained satisfactorily without changing the coefficients for gross photosynthesis (Pg = 0.082 PAR MJ m−2), maintenance (0.242 Pg) or growth respiration (0.003 × total phytomass). Leaf area index and leaf appearance data indicated that the assumptions regarding leaf area development were valid. The observed fluctuations in water content of the top 300 mm of soil were well.
Evaluation of a homogeneous point process description of Arizona thunderstorm rainfall

Rain gage observations of storm events at Walnut Gulch, Arizona, are used to evaluate the Rodriguez-Iturbe and Eagleson (1987) stochastic, point process model of storm events. Five hundred and fifty eight summer storm events are identified over the years 1970–1977 and the parameters of the model estimated by the method of moments for each event as well as for the entire ensemble of events. The model is evaluated by comparing the observed correlation function of the temporally averaged rainfall process to its theoretical analogue.
Undergraduate nursing student's attitudes to learning during clinical practice in different semesters when using a conceptual learning model grounded in a caritative caring perspective - A cross-sectional study.

AIM To describe undergraduate nursing students' attitudes to learning during clinical practice in different semesters when using the conceptual learning model, Model for Improvements in Learning Outcomes (MILO) grounded in a caritative caring perspective. BACKGROUND With the intention to support interlinking between theory and praxis and offer understanding and structure to facilitate learning, MILO, theoretically grounded in hermeneutics and a caritative caring perspective based on ethical values, was implemented. MILO consists of four contextual concepts (peer learning, co-clinical teachers, student-centred and student-active supervision) and four intrapersonal concepts (nursing, a reflective approach, a critical approach, quality and safety). METHODS A descriptive comparative quantitative study design was applied at a Swedish university, 3 hospitals and 13 municipalities in one county. Cross-sectional data collected via a questionnaire developed to assess attitudes to learning related to MILO's contextual and intrapersonal concepts and their applications were used. RESULTS 209 students in semester 3, 4 and 6 participated in 6 different clinical practice courses. In comparison, intrapersonal concepts, that is, the student's own characteristics and abilities were viewed to be of greater value for learning than contextual, that is, organisational-related concepts in all semesters. Understanding the needs of others and reflective learning were rated to be of major importance. Students in semester 3 valued the use of the applications the highest. To be supervised in pairs was rated the lowest in semester 6. Some of the concepts and their applications were to great extent not applied. CONCLUSIONS In all semesters, fundamentals in caritative caring and characteristics and abilities related to the individual student were rated to be of greater importance for learning than environmental support. Providing students opportunities to develop independency seems essential. Use of a learning model such as MILO is dependent on a bearing of a caritative caring culture and a shared understanding between all involved in student learning during clinical practice.
An Analysis of pre and post-Processing Semen Parameters at The Time of Intrauterine Insemination; and The Confounding Effects of Total Motile Sperm Counts on Pregnancy Outcome: A Prospective Cohort Study

Background: This study aims to determine whether pre or post-processing semen parameters obtained during intrauterine insemination (IUI) predict pregnancy when controlling for confounding effects. Materials and Methods: prospective cohort study of 2231 semen analyses was conducted at McGill University of IVF center. Any couples who underwent IUI with partner sperm, over a 2.5-year period, were included. Controlled ovarian stimulation was done with Clomiphene Citrate, Letrozole, or Gonadotropins. Statistical analysis was performed using t tests, two types of stepwise logistic regression, and stepwise discriminant analysis. A comparison of pre and post-processing semen parameters was undertaken to determine the probability of pregnancy. Results: There were significant differences between pregnant and non-pregnant women in post-processing concentration (P=0.043), post-processing total motile sperm count (TMSC) (P=0.049), and post-linearity (P=0.012). However, when variable out-of-the-equation logistic regression or discriminant analysis, which controls for confounding effects between variables, were used, the findings were no longer significant. It was statistically proven that when a variable in the equation logistic regression was employed, post-processing concentration (P=0.005) and post-processing TMSC (P=0.009) remained reliable predictors of pregnancy. Conclusion: Two of three prediction models suggested that TMSC’s relationship with pregnancy is due to confounding factors. One model maintained the validity of the TMSC. While TMSC has always been studied as an important predictor of insemination pregnancies, this finding may be due to confounding effects between semen parameters and therefore requires further investigation as to this relationship.
Functional and anatomical connectivity predict brain stimulation’s mnemonic effects

Abstract Closed-loop direct brain stimulation is a promising tool for modulating neural activity and behavior. However, it remains unclear how to optimally target stimulation to modulate brain activity in particular brain networks that underlie particular cognitive functions. Here, we test the hypothesis that stimulation’s behavioral and physiological effects depend on the stimulation target’s anatomical and functional network properties. We delivered closed-loop stimulation as 47 neurosurgical patients studied and recalled word lists. Multivariate classifiers, trained to predict momentary lapses in memory function, triggered the stimulation of the lateral temporal cortex (LTC) during the study phase of the task. We found that LTC stimulation specifically improved memory when delivered to targets near white matter pathways. Memory improvement was largest for targets near white matter that also showed high functional connectivity to the brain’s memory network. These targets also reduced low-frequency activity in this network, an established marker of successful memory encoding. These data reveal how anatomical and functional networks mediate stimulation’s behavioral and physiological effects, provide further evidence that closed-loop LTC stimulation can improve episodic memory, and suggest a method for optimizing neuromodulation through improved stimulation targeting.
The Levalloisian assemblages of Sindh (Pakistan) and their importance in the Middle Palaeolithic of the Indian Subcontinent

The scope of this paper is to illustrate a series of Levallois assemblages and isolated finds discovered in Sindh (Pakistan), and to discuss their provenance and their relationships with other Middle Palaeolithic assemblages of the Indian Subcontinent. There is no doubt that the Middle Palaeolithic of the study region is no longer represented by “’an enigmatic group of stone industries’ which fall. typologically and stratigrafically, between the hand-axe industries on one side and the microlithic industries on the other” (Allchin 1959: 1). Nevertheless, there are still many problems to solve concerning the interpretation of the assemblages of this period, at least in Sindh. This is mainly due to 1) the scarcity of systematic research. and consequent finds, 2) the absence of multi-period stratified Palaeolithic complexes, 3) the limited number of published collections, and 4) the paucity of Middle/Late Pleistocene environmental data. These are the main reasons why we have to revert to other territories in order to understand the chronology and the cultural significance of the Levallois industries of Sindh.