Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis of the morphology, chemistry and structure of the tibiotarsus, humerus and keel bones in laying hens

ABSTRACT 1. Bone properties are adapted to their specific functions in the animal, so various types of bones develop different characteristics depending on their location in the skeleton. 2. The aim of this research was to compare the chemical composition, mineral characteristics and structural organisation in tibiotarsus, humerus and keel bones as representatives of hen skeletal mineralisation. Complementary analytical techniques, such as X-ray radiography, optical and electron microscopy, thermogravimetry and 2D X-ray diffraction, were used for characterisation. 3. The humerus had a thinner cortex and cortical bone mineral had higher crystallinity and a greater degree of crystal orientation than the tibiotarsus. The humerus generally lacks medullary bone although, when present, it has a higher mineral content than seen in the tibiotarsus. These differences were attributed to the different forces that stimulate bone formation and remodelling. 4. The keel cortical bone had a lower degree of mineralisation than the tibiotarsus or humerus. Its degree of mineralisation decreased from the cranial to the distal end of the bone. This gradient may affect keel mechanical properties, making it more prone to deformation and fractures. 5. Data from studying different bones in laying hens can help to understand mineralisation as well as finding solutions to prevent osteoporosis-related fractures.
Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer

Abstract Mammalian MutY homologue (MUTYH) is an adenine DNA glycosylase that excises adenine inserted opposite 8-oxoguanine (8-oxoG). The inherited variations in human MUTYH gene are known to cause MUTYH-associated polyposis (MAP), which is associated with colorectal cancer. MUTYH is involved in base excision repair (BER) with proliferating cell nuclear antigen (PCNA) in DNA replication, which is unique and critical for effective mutation-avoidance. It is also reported that MUTYH has a Zn-binding motif in a unique interdomain connector (IDC) region, which interacts with Rad9–Rad1–Hus1 complex (9–1–1) in DNA damage response, and with apurinic/apyrimidinic endonuclease 1 (APE1) in BER. However, the structural basis for the BER pathway by MUTYH and its interacting proteins is unclear. Here, we determined the crystal structures of complexes between mouse MUTYH and DNA, and between the C-terminal domain of mouse MUTYH and human PCNA. The structures elucidated the repair mechanism for the A:8-oxoG mispair including DNA replication-coupled repair process involving MUTYH and PCNA. The Zn-binding motif was revealed to comprise one histidine and three cysteine residues. The IDC, including the Zn-binding motif, is exposed on the MUTYH surface, suggesting its interaction modes with 9–1–1 and APE1, respectively. The structure of MUTYH explains how MAP mutations perturb MUTYH function.
Different rates of pollen and seed gene flow cause branch‐length and geographic cytonuclear discordance within Asian butternuts

Summary Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch‐length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation‐by‐distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex‐biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.
Parental suicide attempts and offspring's risk of attempting or dying by suicide: does the timing of a parental suicide attempt matter?

Abstract Background Studies on the transmission of suicide risk have focused on parental history of suicide attempts (SAs), overlooking when the attempt happened. This study examined how the offspring's risk of attempting or dying by suicide varied by the timing of a first parental SA and the sex of the parent who attempted suicide. Methods Participants were 59 469 members of the 1987 Finnish Birth Cohort. The Finnish Hospital Discharge and Cause of Death Registers were the sources for parental and offspring SAs and offspring suicide. Timing of parental SA was coded as before (pre-pregnancy and pregnancy) and after the child's birth [infant/toddler years (0–2 years), childhood (3–11 years), adolescence (12–17 years), and young adulthood (18–26 years)]. Results In the multivariate models, having a parent who attempted suicide increased the offspring's risk of attempting suicide (odds ratio (OR) = 1.77, 95% confidence interval (CI) 1.39–2.25), but not of dying by suicide. Compared to unexposed offspring, those exposed after child's birth were at higher risk of attempting suicide (OR = 1.90, 95% CI 1.46–2.47), specifically when the parent attempted during offspring's childhood, adolescence, and young adulthood. A first maternal SA increased offspring's risk of attempting suicide regardless of the timing. Conclusions The impact of a parental SA on offspring's risk of attempting suicide differed depending on the timing and sex of the parent who attempted suicide, suggesting that the transmission of suicide risk may occur through genetic as well as environmental factors. Our findings call for an intergenerational approach in suicide risk assessment.
Do glia provide the link between low‐grade systemic inflammation and normal cognitive ageing? A 1H magnetic resonance spectroscopy study at 7 tesla

Low‐grade systemic inflammation contributes to ageing‐related cognitive decline, possibly by triggering a neuroinflammatory response through glial activation. Using proton magnetic resonance spectroscopy (1H‐MRS) at 7T in normal human individuals from 18 to 79 years in a cross‐sectional study, we previously observed higher regional levels of myo‐inositol (mIns), total creatine (tCr) and total choline (tCho) in older than younger age groups. Moreover, visuo‐spatial working memory (vsWM) correlated negatively with tCr and tCho in anterior cingulate cortex (ACC) and mIns in hippocampus and thalamus. As mIns, tCr and tCho are higher in glia than neurons, this suggest a potential in vivo connection between cognitive ageing and higher regional levels of glia‐related metabolites. In the present study, we tested whether these metabolic differences may be related to low‐grade systemic inflammation. In the same individuals, plasma concentrations of the proinflammatory markers C‐reactive protein (CRP), interleukin 8 (IL‐8), and tumour necrosis factor α (TNF‐α) were measured on the same day as 1H‐MRS assessments. We tested whether CRP, IL‐8, and TNF‐α concentrations correlated with the levels of glia‐related metabolites. CRP and IL‐8, but not TNF‐α, were higher in older (69–79 years) than younger (18–26 years) individuals. CRP correlated positively with thalamic mIns and negatively with vsWM. IL‐8 correlated positively with ACC tCho and hippocampal mIns, but not with vsWM. Mediation analysis revealed an indirect effect of IL‐8 on vsWM via ACC tCho. Together, these findings corroborate the role of glial cells, perhaps via their role in neuroinflammation, as part of the neurobiological link between systemic inflammation and cognitive ageing.
A path toward concurrent biofortification and cadmium mitigation in plant-based foods.

Millions of people are anemic due to inadequate consumption of foods rich in iron and zinc. Plant-based foods provide most of our dietary nutrients but may also contain the toxic heavy metal cadmium (Cd). A low level of Cd silently enters the body through the diet. Once ingested, Cd may remain for decades. Hence, prolonged intake of Cd-containing foods endangers human health. Research that leads towards micronutrient enrichment and mitigation of Cd in foods has therefore dual significance for human health. The breeding of Cd-tolerant cultivars may enable them to grow on Cd-polluted soils; however, they may not yield Cd-free foods. Conversely, sequestration of Cd in roots can prevent its accumulation in grains, but this mechanism also retains nutrients, hence counteracting biofortification efforts. A specific restriction of the Cd absorption capacity of crops would prevent Cd entry into the plant system while maintaining micronutrient accumulation and may thus be a solution of the dilemma. After recapitulating existing strategies employed for the development of Cd-tolerant and biofortified cultivars, this viewpoint elaborates alternative approaches based on directed evolution and genome editing strategies for excluding Cd while enriching micronutrients in plant foods, which will concurrently help to eradicate malnutrition and prevent Cd intoxication.
Semiparametric estimation of the proportional rates model for recurrent events data with missing event category

Proportional rates models are frequently used for the analysis of recurrent event data with multiple event categories. When some of the event categories are missing, a conventional approach is to either exclude the missing data for a complete-case analysis or employ a parametric model for the missing event type. It is well known that the complete-case analysis is inconsistent when the missingness depends on covariates, and the parametric approach may incur bias when the model is misspecified. In this paper, we aim to provide a more robust approach using a rate proportion method for the imputation of missing event types. We show that the log-odds of the event type can be written as a semiparametric generalized linear model, facilitating a theoretically justified estimation framework. Comprehensive simulation studies were conducted demonstrating the improved performance of the semiparametric method over parametric procedures. Multiple types of Pseudomonas aeruginosa infections of young cystic fibrosis patients were analyzed to demonstrate the feasibility of our proposed approach.
A Quantitative Analysis of Anions and pH on the Growth of Bimetallic Nanostructures

Symmetrically branched and shape-controlled alloyed nanocrystals composed of Au and Pd are synthesized via seed-mediated coreduction, in which the two metals are simultaneously deposited onto Au seeds. Here, a qualitative evaluation of morphology development (obtained via SEM of product from reaction aliquots) is coupled with a quantitative analysis of metal deposition rates (obtained via ICP-MS of the same samples) to elucidate the roles of anions and pH in bimetallic nanostructure formation. Different anion environments and total precursor concentration were found to influence metal deposition rates and nanostructure morphology. In contrast, reaction pH did not alter the deposition rates significantly despite dramatic changes in morphology. The latter is surprising given the often-cited pH-dependent reduction process in similar systems. These experiments are a first effort at quantitatively analyzing the kinetics of metal deposition in a bimetallic system, where understanding the shape-directing effects.
Prenatal androgen influences on the brain: A review, critique, and illustration of research on congenital adrenal hyperplasia

Sex hormones, especially androgens, contribute to sex and gender differences in the brain and behavior. Organizational effects are particularly important because they are thought to be permanent, reflecting hormone exposure during sensitive periods of development. In human beings, they are often studied with natural experiments in which sex hormones are dissociated from other biopsychosocial aspects of development, such as genes and experiences. Indeed, the greatest evidence for organizational effects on sex differences in human behavior comes from studies of females with congenital adrenal hyperplasia (CAH), who have heightened prenatal androgen exposure, female‐typical rearing, and masculinized toy play, activity and career interests, spatial skills, and some personal characteristics. Interestingly, however, neuroimaging studies of females with CAH have revealed few neural mechanisms underlying these hormone‐behavior links, with the exception of emotion processing; studies have instead shown reduced gray matter volumes and reduced white matter integrity most consistent with other disease‐related processes. The goals of this narrative review are to: (a) describe methods for studying prenatal androgen influences, while offering a brief overview of behavioral outcomes; (b) provide a critical methodological review of neuroimaging research on females with CAH; (c) present an illustrative analysis that overcomes methodological limitations of previous work, focusing on person‐specific neural reward networks (and their associations with sensation seeking) in women with CAH and their unaffected sisters in order to inform future research questions and approaches that are most likely to reveal organizational hormone effects on brain structure and function.
Electronic structures and anisotropic carrier mobilities of monolayer ternary metal iodides MLaI5 (M=Mg, Ca, Sr, Ba)

Exploiting two-dimensional (2D) materials with natural band gaps and anisotropic quasi-one-dimensional (quasi-1D) carrier transport character is essential in high-performance nanoscale transistors and photodetectors. Herein, the stabilities, electronic structures and carrier mobilities of 2D monolayer ternary metal iodides MLaI5 (M = Mg, Ca, Sr, Ba) have been explored by utilizing first-principles calculations combined with numerical calculations. It is found that exfoliating MLaI5 monolayers are feasible owing to low cleavage energy of 0.19–0.21 J m−2 and MLaI5 monolayers are thermodynamically stable based on phonon spectra. MLaI5 monolayers are semiconductors with band gaps ranging from 2.08 eV for MgLaI5 to 2.51 eV for BaLaI5. The carrier mobility is reasonably examined considering both acoustic deformation potential scattering and polar optical phonon scattering mechanisms. All MLaI5 monolayers demonstrate superior anisotropic and quasi-1D carrier transport character due to the striped structures. In particular, the anisotropic ratios of electron and hole mobilities along different directions reach hundreds and tens for MLaI5 monolayers, respectively. Thus, the effective electron–hole spatial separation could be actually achieved. Moreover, the absolute locations of band edges of MLaI5 monolayers have been aligned. These results would provide fundamental insights for MLaI5 monolayers applying in nano-electronic and optoelectronic devices.
Oops! I Did it Again: The Psychology of Everyday Action Slips

We have all had the experience of everyday mistakes like distractedly pouring orange juice into our cereal bowl rather than the milk or inadvertently continuing on our regular route home rather than stopping at the store as we had planned. These so-called "action slips" (Reason, 1984a) are characterized as failures to execute one's intention arising in habitual or highly learned action sequences. This paper argues that a proper understanding of slips, and thus action more generally, requires an understanding of the control structure that implements an agent's guiding intentions. Central to this structure are motor representations that are active downstream of intention and attentional processes that ensure that they reliably implement the intentions they serve.
Lack of fit with the neighbourhood social environment as a risk factor for psychosis – a national cohort study

Abstract Background Many studies report an ethnic density effect whereby psychosis incidence among ethnic minority groups is higher in low co-ethnic density areas. It is unclear whether an equivalent density effect applies with other types of socioeconomic disadvantages. Methods We followed a population cohort of 2 million native Danes comprising all those born on 1st January 1965, or later, living in Denmark on their 15th birthday. Socioeconomic disadvantage, based on parents' circumstances at age 15 (low income, manual occupation, single parent and unemployed), was measured alongside neighbourhood prevalence of these indices. Results Each indicator was associated with a higher incidence of non-affective psychosis which remained the same, or was slightly reduced, if neighbourhood levels of disadvantage were lower. For example, for individuals from a low-income background there was no difference in incidence for those living in areas where a low-income was least common [incidence rate ratio (IRR) 1.01; 95% confidence interval (CI) 0.93–1.10 v. those in the quintile where a low income was most common. Typically, differences associated with area-level disadvantage were the same whether or not cohort members had a disadvantaged background; for instance, for those from a manual occupation background, incidence was lower in the quintile where this was least v. most common (IRR 0.83; 95% CI 0.71–0.97), as it was for those from a non-manual background (IRR 0.77; 95% CI 0.67–0.87). Conclusion We found little evidence for group density effects in contrast to previous ethnic density studies. Further research is needed with equivalent investigations in other countries to see if similar patterns are observed.
Cytokines: Application in recurrence appraisal for differentiated thyroid carcinoma and their relation with radioiodine ablation

The limitations in discriminating preablation disease‐active status of differentiated thyroid carcinoma (DTC) still represent a major challenge to radioiodine dose management. Cytokines, the small protein signaling molecules that constitute the thyroid tumor microenvironment, play significant roles in the facilitation of intercellular communication and the control of tumorigenesis. Also, more attention should be paid to the molecular events within the innate and adaptive immune systems that occur after the organism being exposed to ionizing radiation. Therefore, we implemented a study of 260 patients with DTC in thyroid hormone withdrawal status who were treated with total thyroidectomy to explore the relationship between cytokines and recurrence/active disease status. Besides, we made a cross‐sectional study to analyze pre‐ and post‐ablation serum concentration of cytokines of 86 patients with DTC. There was a relationship between clinicohistopathological characteristics of patients with DTC and the presence of cytokines. It is noteworthy that patients with recurrence/active disease were at a higher serum interleukin‐2 receptor (IL‐2R) level than the disease‐free patients (213.59 ± 75.43 pg/ml vs. 186.80 ± 77.40 pg/ml, P = 0.005). Positive correlation was observed between serum IL‐2R and thyroglobulin (Tg) (P = 0.003). We also found significant changes in the cytokine profile after radioiodine ablation, including the decrease of tumor necrosis factor‐α and IL‐8 (P < 0.001, P < 0.001, respectively), and increase of IL‐2R (P < 0.001). Thus, we suggest that serum IL‐2R may assist in evaluating the disease status during the post‐thyroidectomy follow‐up and radioiodine therapy has an immunoregulatory effect on serum cytokines.
Early Results of a Novel Intramedullary Fixation Device for Proximal Fifth Metatarsal Fractures

Background Proximal fifth metatarsal fractures are commonly treated surgically due to their poor healing capacity. While intramedullary screws may be the most popular operative treatment choice, newer fixation methods continue to develop. We present a case series utilizing a novel intramedullary fixation device for proximal fifth metatarsal fractures. To our knowledge, no other study in the literature has assessed the safety and efficacy of this fixation method. Methods A retrospective analysis was performed for 16 patients with proximal fifth metatarsal fractures who underwent fixation with the same novel intramedullary device. Patient charts were reviewed for fracture union, plantar fracture gapping, time to weight-bearing, refracture, perioperative complications, and secondary surgeries. Results Sixteen patients with an average age of 43.3 years underwent fixation with this novel device from 2015 to 2020. Mean follow-up was 32.4 weeks. Fifteen of the 16 patients achieved radiographic union at a mean of 8.9 weeks. One patient suffered a nonunion. Mean time to full weight-bearing in, and out of, a walking boot was 6.4 and 9.8 weeks, respectively, for healed fractures. Mean plantar fracture gap improved from 1.22 mm to 0.88 mm following surgery. There were zero infections, refractures, or hardware complications. Three patients suffered iatrogenic fracture during implant insertion. Conclusion To our knowledge, this is the first report of early results for this novel intramedullary device. Excellent union rates, acceptable time to weight-bearing, and a low complication profile can be achieved. Based on our findings, we propose a safe and effective treatment option for proximal fifth metatarsal fractures. Levels of Evidence Level IV: Clinical case series
Detection of Postcolonoscopy Colorectal Neoplasia by Multi-target Stool DNA

INTRODUCTION: Significant variability between colonoscopy operators contributes to postcolonoscopy colorectal cancers (CRCs). We aimed to estimate postcolonoscopy colorectal neoplasia (CRN) detection by multi-target stool DNA (mt-sDNA), which has not previously been studied for this purpose. METHODS: In a retrospective cohort of patients with +mt-sDNA and completed follow-up colonoscopy, positive predictive value (PPV) for endpoints of any CRN, advanced adenoma, right-sided neoplasia, sessile serrated polyps (SSP), and CRC were stratified by the time since previous colonoscopy (0–9, 10, and ≥11 years). mt-sDNA PPV at ≤9 years from previous average-risk screening colonoscopy was used to estimate CRN missed at previous screening colonoscopy. RESULTS: Among the 850 studied patients with +mt-sDNA after a previous negative screening colonoscopy, any CRN was found in 535 (PPV 63%). Among 107 average-risk patients having +mt-sDNA ≤9 years after last negative colonoscopy, any CRN was found in 67 (PPV 63%), advanced neoplasia in 16 (PPV 15%), right-sided CRN in 48 (PPV 46%), and SSP in 20 (PPV 19%). These rates were similar to those in 47 additional average risk persons with previous incomplete colonoscopy and in an additional 68 persons at increased CRC risk. One CRC (stage I) was found in an average risk patient who was mt-sDNA positive 6 years after negative screening colonoscopy. DISCUSSION: The high PPV of mt-sDNA 0–9 years after a negative screening colonoscopy suggests that lesions were likely missed on previous examination or may have arisen de novo. mt-sDNA as an interval test after negative screening colonoscopy warrants further study.