Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy and its mediated mitochondrial quality control maintain pollen tube growth and male fertility in Arabidopsis

ABSTRACT Macroautophagy/autophagy, a major catabolic pathway in eukaryotes, participates in plant sexual reproduction including the processes of male gametogenesis and the self-incompatibility response. Rapid pollen tube growth is another essential reproductive process that is metabolically highly demanding to drive the vigorous cell growth for delivery of male gametes for fertilization in angiosperms. Whether and how autophagy operates to maintain the homeostasis of pollen tubes remains unknown. Here, we provide evidence that autophagy is elevated in growing pollen tubes and critically required during pollen tube growth and male fertility in Arabidopsis. We demonstrate that SH3P2, a critical non-ATG regulator of plant autophagy, colocalizes with representative ATG proteins during autophagosome biogenesis in growing pollen tubes. Downregulation of SH3P2 expression significantly disrupts Arabidopsis pollen germination and pollen tube growth. Further analysis of organelle dynamics reveals crosstalk between autophagosomes and prevacuolar compartments following the inhibition of phosphatidylinositol 3-kinase. In addition, time-lapse imaging and tracking of ATG8e-labeled autophagosomes and depolarized mitochondria demonstrate that they interact specifically via the ATG8-family interacting motif (AIM)-docking site to mediate mitophagy. Ultrastructural identification of mitophagosomes and two additional forms of autophagosomes imply that multiple types of autophagy are likely to function simultaneously within pollen tubes. Altogether, our results suggest that autophagy is functionally crucial for mediating mitochondrial quality control and canonical cytoplasm recycling during pollen tube growth. Abbreviations: AIM: ATG8-family interacting motif; ATG8: autophagy related 8; ATG5: autophagy related 5; ATG7: autophagy related 7; BTH: acibenzolar-S-methyl; DEX: dexamethasone; DNP: 2,4-dinitrophenol; GFP: green fluorescent protein; YFP: yellow fluorescent protein; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PVC: prevacuolar compartment; SH3P2: SH3 domain-containing protein 2.
Trends in Clostridioides difficile prevalence, mortality, severity, and age composition during 2003–2014, the national inpatient sample database in the US

Abstract Background Clostridioides difficile (formerly known as Clostridium difficile) infection (CDI) is one of the most prevalent healthcare-associated infections in the United States (US). In the early 2000s, CDI emerged as a great threat with increasing prevalence, mortality, and severity, especially in advanced age. We investigated the US national trends in in-hospital CDI prevalence, mortality, severity, and age composition from 2003 to 2014. Methods We identified the patients with CDI using the national inpatient sample data from 2003 to 2014. We performed Poisson regression model and Kendall’s tau-b correlation test for our analyses. Results Adjusted overall CDI prevalence did not significantly change during 2003–2014. In-hospital mortality of overall CDI did not significantly change during 2003–2008, then significantly decreased during 2008–2014. Severity of overall CDI significantly increased during 2003–2008, then decreased during 2008–2014. The proportions of patients with age 65 years decreased in CDI prevalence, mortality, and severity during 2003–2014. Conclusions Compared to the earlier years 2003–2008, overall CDI outcome improved in the later years 2008–2014. Younger patients increasingly contributed to CDI prevalence, mortality, and severity during 2003–2014. More studies to understand underlying driving forces of changes in CDI trends are warranted to mitigate CDI.
Clinical characteristics of medically hospitalized youth with anorexia nervosa/atypical anorexia nervosa and premorbid overweight/obesity

ABSTRACT Youth with anorexia nervosa (AN) or atypical anorexia nervosa (AAN) and premorbid overweight/obesity are particularly vulnerable to diagnostic delays, yet research about this patient subset is lacking. This study aimed to compare mental health and demographic characteristics of patients with AN/AAN and premorbid overweight/obesity to patients with premorbid normal weight. Retrospective chart review identified 253 patients (aged 10–22) hospitalized for medical complications of AN/AAN between 2013 and 2020, including 29.6% (n = 75) with and 70.4% (n = 178) without premorbid overweight/obesity. Analyses revealed that patients with AN/AAN and premorbid overweight/obesity were more often cisgender male (24% vs. 8.4%), diagnosed with AAN (62.7% vs. 32%), and had lost a greater percent of body weight (29% vs. 16.4%) than premorbid normal weight counterparts. No significant differences were found for illness duration (10.1 months vs 9.3 months), psychiatric comorbidities (42.7% vs. 32.2%) or psychotropic medication use (25.3% vs. 19.2%), past mental health treatment (44.6% vs. 37.5%), or family history of eating disorders (22.7% vs. 20.8%). Our findings suggest that when relying on historical records, patients hospitalized for medical complications of AN/AAN have similar characteristics across the weight spectrum.
Reply to Kodner et al.: Fundamental misunderstanding of both model and methods

Our recent work (1) shows a program-learning model can acquire some key structures in natural language, including recursive hierarchies and patterns that require more than context-free capacities (2). Kodner et al.’s (KCY) commentary (3) is based on several fundamental misunderstandings. Most notably, they claim that our “model transforms candidate hypotheses into probabilistic context-free grammars that are evaluated against the training data via Bayesian inference. ” This is unambiguously incorrect: At no point does our model convert hypotheses into probabilistic context-free grammars. Not only does it not do that, but that approach could not work because we show that the model can learn languages that are not context-free: No method of comparing context-free grammars could learn the languages our model succeeds on. Our model compares programs, not grammars, and we showed examples of these programs in the paper. KCY claim we conceive of “language as strings” and we fail to recognize that language has structure. This is another fundamental misunderstanding. It is true that the data provided to the model are strings (sequences of characters), following prior work on learnability, but the model uses the strings to discover structure, much like a linguist would. Finding latent structure behind strings is the only way for the model to generalize beyond what it has seen, which our results document it does. KCY contend that our analysis method is flawed because an n-gram model can show high performance on some languages when following our methods. Their interpretation is not correct. KCY only examined performance of an n-gram model on finite-state languages (figure 1 of ref. 3), which are precisely languages that an n-gram model can represent. So, of course an n-gram model can do well on their examples. In fact, no evaluation metric could show that n-gram models are poor on these languages because, simply, they are not. One has to look at nonfinite state languages, where our evaluation scheme shows an n-gram model fails (Fig. 1). Thus, our evaluation does exactly what it should: It scores an n-gram model high on languages they can learn (figure 1 of ref. 3) and low on languages they cannot learn (Fig. 1). The same metric shows that our model learns everything from finite sets to context-sensitive grammars. Finally, KCY grab onto our statement that people do not necessarily use the same methods as our implementation. Ours is a standard Marr (4) computational-level analysis: We hoped to formalize the problem people solve (Bayesian selection of generative processes) without necessarily knowing how they solve it. Our more modest claim is warranted because there is no evidence about how children solve this problem. The insight of Marr also answers KYC’s final question of how the model helps us understand acquisition. The model shows that learning a generating process for languages is possible, xx Dyck abc ab abc xx
Romantic relationship quality and functioning for individuals with clinical and sub-clinical social anxiety: a scoping review

Abstract Background Social Anxiety Disorder (SAD) is associated with pervasive functional impairments and chronicity. Romantic relationship functioning and quality for individuals with SAD has been previously explored but existing studies have not been synthesised. Aims This scoping review charted existing literature regarding the quality and functioning of romantic relationships for people with SAD and high sub-clinical social anxiety (SA). Methods The review used a scoping approach to explore the current evidence base relating to SA, romantic relationship quality and functioning. Articles published in English after 1980 that reported either clinical or high sub-clinical SA were eligible. Double screening, data extraction, quality assessment, and thematic analysis of studies was conducted. Results 50 studies from 46 articles were identified, involving a range of community, college, adolescent, and clinical samples. Thematic analysis identified four themes; Relationship Quality, Satisfaction and Commitment; Communication and Self-Disclosure; Conflict, Social Support and Trust; Intimacy, Closeness and Sexual Satisfaction. Conclusions The review highlights that evidence relating to romantic relationship functioning for individuals with SAD and high sub-clinical SA is heterogeneous, with relationship initiation in particular relatively under-explored. Further research is required to elucidate key constructs and interpersonal processes related to relationship functioning, and to inform treatment approaches with this group.
Emerging green cell disruption techniques to obtain valuable compounds from macro and microalgae: a review

Abstract In the modern era, macro-microalgae attract a strong interest across scientific disciplines, owing to the wide application of these cost-effective valuable bioresources in food, fuel, nutraceuticals, and pharmaceuticals etc. The practice of eco-friendly extraction techniques has led scientists to create alternative processes to the conventional methods, to enhance the extraction of the key valuable compounds from macro-microalgae. This review narrates the possible use of novel cell disruption techniques, including use of ionic liquid, deep eutectic solvent, surfactant, switchable solvents, high voltage electrical discharge, explosive decompression, compressional-puffing, plasma, and ozonation, which can enable the recovery of value added substances from macro-microalgae, complying with the principles of green chemistry and sustainability. The above-mentioned innovative techniques are reviewed with respect to their working principles, benefits, and possible applications for macro-microalgae bioactive compound recovery and biofuel. The benefits of these techniques compared to conventional extraction methods include shorter extraction time, improved yield, and reduced cost. Furthermore, various combinations of these innovative technologies are used for the extraction of thermolabile bioactive compounds. The challenges and prospects of the innovative extraction processes for the forthcoming improvement of environmentally and cost-effective macro-microalgal biorefineries are also explained in this review.
Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota

Significance The spatial structure of microbial communities can influence their ecological and evolutionary dynamics. Gut bacteria in particular experience large variations in growth conditions along the colon. However, little is known about how these spatial growth processes influence the long-term genetic turnover of the gut community. Here we develop a mathematical framework to predict how stochastic evolutionary forces emerge from simple models of bacterial growth in the intestinal lumen. This framework describes how fluid flow and growth combine to shape the frequencies of mutations at different spatial locations. We show that over longer timescales, these mutation dynamics can often be captured by coarse-grained models that lack explicit spatial structure, even when there is strong spatial variation in species-level composition.
Association of Thrombin Generation With Leukocyte Inflammatory Profile in Patients With Acute Ischemic Stroke

Background and Objectives Thrombosis is central to the pathogenesis of acute ischemic stroke, with higher thrombin generation being associated with increased stroke risk. The immune system may contribute to thrombin generation in stroke and thus may offer novel strategies for stroke prevention. This study addresses the research question regarding the relationship of thrombin generation to leukocyte gene expression in patients with acute ischemic stroke. Methods We isolated RNA from whole blood and examined the relationship to thrombin generation capacity in patients with acute ischemic stroke. Due to its effects on thrombin generation, patients on anticoagulants were excluded from the study. The relationship of gene expression with peak thrombin was evaluated by analysis of covariance across peak thrombin quartiles adjusted for sex and age. Results In 97 patients with acute ischemic stroke, peak thrombin was variable, ranging from 252.0 to 752.4 nM. Increased peak thrombin was associated with differences in thromboinflammatory leukocyte gene expression, including a decrease in ADAM metallopeptidase with thrombospondin type 1 motif 13 and an increase in nuclear factor κB (NF-κB)–activating protein, protein disulfide isomerase family A member 5, and tissue factor pathway inhibitor 2. Pathways associated with peak thrombin included interleukin 6 signaling, thrombin signaling, and NF-κB signaling. A linear discriminant analysis model summarizing the immune activation associated with peak thrombin in a first cohort of stroke could distinguish patients with low peak thrombin from high peak thrombin in a second cohort of 112 patients with acute ischemic stroke. Discussion The identified genes and pathways support a role of the immune system contributing to thrombus formation in patients with stroke. These may have relevance to antithrombotic strategies for stroke prevention.
Periodontitis prevalence in patients with ulcerative colitis and Crohn's disease ‐ PPCC: A case–control study

Abstract Aim The aim of this questionnaire‐based case–control study was to assess whether self‐reported oral health and periodontitis in patients with ulcerative colitis (UC) and Crohn's disease (CD) differ from those in matched controls without inflammatory bowel disease (IBD). Materials and Methods A survey including questions on general anamnestic information, IBD diagnosis, and oral health was distributed online. Self‐perceived overall health of teeth and gums, severe periodontitis, and tooth loss were defined as outcome parameters. Results Analyses were based on answers from 1108 patients with IBD and 3429 controls. Patients with IBD reported significantly worse oral health and more periodontal problems compared to controls. Regression analyses corrected for relevant confounders showed significantly increased odds for fair or poor self‐perceived overall health of teeth and gums (odds ratio [OR] 2.147 and 2.736, respectively) and for severe periodontitis (OR 1.739 and 2.574, respectively) for patients with UC and CD compared to controls; patients with CD presented additionally 91% higher odds for having <20 remaining teeth. Conclusion Patients with UC and CD have significantly increased odds for worse self‐perceived oral health and severe periodontitis compared to controls, with the former being more severely affected and losing more teeth. It is strongly recommended that patients with IBD are kept under close surveillance to prevent periodontitis development and/or mitigate its progression.
Perceptual Data Augmentation for Biomedical Coronary Vessel Segmentation

Sufficient annotated data is critical to the success of deep learning methods. Annotating for vessel segmentation in X-ray coronary angiograms is extremely difficult because of the small and complex structures to be processed. Although unsupervised domain adaptation methods can be utilized to alleviate the annotation burden by using data in other domains, e.g., eye fundus images, these methods cannot perform well due to the characteristic of medical images. Data augmentation can help improve the similarity of source domain and target domain in unsupervised domain adaptation tasks. Existing data augmentation methods play a limited role in improving domain adaptation performance, especially for special medical image segmentation tasks. In this paper, we propose an effective perceptual data augmentation method to improve the similarity between eye fundus images and coronary angiograms by synthesizing virtual samples. Auto Foreground Augment method is designed to search for geometric transformations that improve the similarity between foreground vessels of eye fundus images and coronary angiograms. The Haar Wavelet-Based Perceptual Similarity Index is utilized to guide the synthesis of virtual samples in foreground and background mixup. Extensive experiments show that our data augmentation method can synthesize high-quality virtual samples and thus improve the domain adaptation performance. To our best knowledge, this is the first work to apply perceptual data augmentation to vessel segmentation in coronary angiograms.
Cognition in zero gravity: Effects of non-terrestrial gravity on human behaviour

As humanity prepares for deep space exploration, understanding the impact of spaceflight on bodily physiology is critical. While the effects of non-terrestrial gravity on the body are well established, little is known about its impact on human behaviour and cognition. Astronauts often describe dramatic alterations in sensorimotor functioning, including orientation, postural control, and balance. Changes in cognitive functioning as well as in socio-affective processing have also been observed. Strikingly, no comprehensive theoretical model exists to outline the impact of non-terrestrial gravity on behaviour. Here, we have reviewed the key literature across the last 10 years and explored the impact of non-terrestrial gravity across three key functional domains: sensorimotor functioning, cognition, and socio-affective processing. We have proposed and preliminary validated a neurocognitive model to account for the effects of non-terrestrial gravity in these domains. Understanding the impact of non-terrestrial gravity on human behaviour has never been timelier and it will help mitigate against risks in both commercial and non-commercial spaceflight.
Association of serum high-sensitivity C reactive protein with risk of mortality in an Asian population: the Health Examinees cohort

Objectives This study aimed to examine the association of high-sensitivity C reactive protein (hsCRP) with mortality risk and the attenuated effect of non-communicable disease history (NCDhistory) on the association. Design Prospective cohort study. Setting Health Examinees cohort. Participants A total of 41 070 men and 81 011 women aged ≥40 years were involved (follow-up: 6.8 years). Outcome measures Data and cause of death occurring until 31 December 2015 were confirmed by death statistics from the National Statistical Office. We conducted advanced analysis after stratification by NCDhistory and sensitivity analysis after excluding death before 1 or 2 years from recruitment. Cox proportional hazard and restricted cubic spline models were used to assess the association. Results The association between serum hsCRP and risk of all-cause mortality was observed with strong linearity in both genders and was not influenced by NCDhistory. The association of serum hsCRP with risk of cancer mortality was not observed in women with NCDhistory, but the association with risk of cardiovascular disease (CVD) mortality was predominantly observed in men with NCDhistory. Conclusions This study suggests a dose–response association of hsCRP with mortality risk, including cancer and CVD mortality, in Koreans with low serum hsCRP, although the association with cancer and CVD mortality risk could be influenced by gender and NCDhistory.
COVID-19: Factors Predicting Depressive Symptoms in People Aging With Long-Term Physical Disabilities

The mental health impact of the COVID-19 pandemic may be greater than that of the viral infection. This impact is likely greater for disadvantaged groups such as people with long-term physical disabilities (PwLTPD). This cross-sectional study used a multiple linear regression model to examine factors associated with depressive symptoms and to understand their relative importance during the onset of the COVID-19 pandemic. The model explained 58% of the variance in depressive symptoms. Anxiety was the most important predictor, accounting for 8% of variance. Higher levels of anxiety, loneliness, and financial stress; prior diagnosis of depression; and non-Black race predicted a higher level of depressive symptoms in PwLTPD during the onset of the COVID-19 pandemic. Occupational therapy practitioners should strategically acknowledge predictors of depression that cannot be modified and actively address those that can be modified through evidence-based interventions to improve depressive symptoms in PwLTPD.
Nocturnal hypoxemia, blood pressure, vascular status and chronic mountain sickness in the highest city in the world

Abstract Introduction Chronic mountain sickness (CMS) is a condition characterized by excessive erythrocytosis in response to chronic hypobaric hypoxia. CMS frequently triggers cardiorespiratory diseases such as pulmonary hypertension and right or left heart failure. Ambient hypoxia might be further amplified night-time by intermittent hypoxia related to sleep-disordered breathing (SDB) so that sleep disturbance may be an important feature of CMS. Our aim was to characterize in a cross-sectional study nocturnal hypoxaemia, SDB, blood pressure (BP), arterial stiffness and carotid intima-media thickness (CIMT) in highlanders living at extreme altitude. Methods Men aged 18 to 55 years were prospectively recruited. Home sleep apnoea test, questionnaires (short-form health survey; Montreal cognitive assessment; Pittsburgh Sleep Questionnaire Index and the Insomnia severity index), 24-h ambulatory BP monitoring, CIMT and arterial stiffness were evaluated in 3 groups: i) Andean lowlanders (sea-level); ii) highlanders living at 3,800 m and iii) highlanders living at 5,100 m. Analyses were conducted in sub-groups according to 1) CMS severity 2) healthy subjects living at the three different altitude. Results Ninety-two males were evaluated at their living altitudes. Among the 54 highlanders living at 5,100 m, subjects with CMS showed lower mean nocturnal oxygen saturation (SpO2), SpO2 nadir, lower pulse wave velocity and higher nocturnal BP variability than those with no-CMS. Lower nocturnal SpO2 nadir was associated with higher CMS severity (ß= −0.14, p=.009). Among the 55 healthy subjects, healthy highlanders at 5,100 m were characterized by lower scores on quality of life and sleep quality scales and lower mean SpO2 compared to lowlanders. Conclusions Lower nocturnal SpO2 and higher nocturnal BP variability are associated with CMS severity in individuals living permanently at high altitude. The role of lower SpO2 and higher nocturnal BP variability in the cardiovascular progression of CMS and in the overall prognosis of the disease need to be evaluated in further studies.