Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian clock genes and sleep homeostasis

Circadian and sleep‐homeostatic processes both contribute to sleep timing and sleep structure. Elimination of circadian rhythms through lesions of the suprachiasmatic nuclei (SCN), the master circadian pacemaker, leads to fragmentation of wakefulness and sleep but does not eliminate the homeostatic response to sleep loss as indexed by the increase in EEG delta power. In humans, EEG delta power declines during sleep episodes nearly independently of circadian phase. Such observations have contributed to the prevailing notion that circadian and homeostatic processes are separate but recent data imply that this segregation may not extend to the molecular level. Here we summarize the criteria and evidence for a role for clock genes in sleep homeostasis. Studies in mice with targeted disruption for core circadian clock genes have revealed alterations in circadian rhythmicity as well as changes in sleep duration, sleep structure and EEG delta power. Clock‐gene expression in brain areas outside the SCN, in particular the cerebral cortex, depends to a large extent on prior sleep–wake history. Evidence for effects of clock genes on sleep homeostasis has also been obtained in Drosophila and humans, pointing to a phylogenetically preserved pathway. These findings suggest that, while within the SCN clock genes are utilized to set internal time‐of‐day, in the forebrain the same feedback circuitry may be utilized to track time spent awake and asleep. The mechanisms by which clock‐gene expression is coupled to the sleep–wake distribution could be through cellular energy charge whereby clock genes act as energy sensors. The data underscore the interrelationships between energy metabolism, circadian rhythmicity, and sleep regulation.
Planar cell movements and oriented cell division during early primitive streak formation in the mammalian embryo

Formation of the mammalian primitive streak appears to rely on cell proliferation to a minor extent only, but compensating cell movements have not yet been directly observed. This study analyses individual cell migration and proliferation simultaneously, using multiphoton and differential interference contrast time‐lapse microscopy of late pregastrulation rabbit blastocysts. Epiblast cells in the posterior gastrula extension area accumulated medially and displayed complex planar movements including U‐turns and a novel type of processional cell movement. In the same area metaphase plates tended to be aligned parallel to the anterior–posterior axis, and statistical analysis showed that rotations of metaphase plates causing preferred orientation were near‐complete 8 min before anaphase onset; in some cases, rotations were strikingly rapid, achieving up to 45° per min. The mammalian primitive streak appears to be formed initially with its typically minimal anteroposterior elongation by a combination of oriented cell divisions with dedicated planar cell movements. Developmental Dynamics 240:1905–1916, 2011. © 2011 Wiley‐Liss, Inc.
Spring-loaded inverted pendulum goes through two contraction-extension cycles during the single-support phase of walking

ABSTRACT Despite the overall complexity of legged locomotion, the motion of the center of mass (COM) itself is relatively simple, and can be qualitatively described by simple mechanical models. In particular, walking can be qualitatively modeled by a simple model in which each leg is described by a spring-loaded inverted pendulum (SLIP). However, SLIP has many limitations and is unlikely to serve as a quantitative model. As a first step to obtaining a quantitative model for walking, we explored the ability of SLIP to model the single-support phase of walking, and found that SLIP has two limitations. First, it predicts larger horizontal ground reaction forces (GRFs) than empirically observed. A new model – angular and radial spring-loaded inverted pendulum (ARSLIP) – can overcome this deficit. Second, although the leg spring (surprisingly) goes through contraction-extension-contraction-extensions (CECEs) during the single-support phase of walking and can produce the characteristic M-shaped vertical GRFs, modeling the single-support phase requires active elements. Despite these limitations, SLIP as a model provides important insights. It shows that the CECE cycling lengthens the stance duration allowing the COM to travel passively for longer, and decreases the velocity redirection between the beginning and end of a step. Summary: We quantitatively evaluate a simple model for human walking based on two-spring and find that this model describes many features of human walking.
Draft Genome Sequence of Amphirosellinia nigrospora JS-1675, an Endophytic Fungus from Pteris cretica

The fungus Amphirosellinia nigrospora strain JS-1675 has been reported to exert antimicrobial effects against various plant-pathogenic bacteria and fungi. Here, we report the draft genome sequence of A. nigrospora for the first time. ABSTRACT The fungus Amphirosellinia nigrospora strain JS-1675 has been reported to exert antimicrobial effects against various plant-pathogenic bacteria and fungi. Here, we report the draft genome sequence of A. nigrospora for the first time. The assembly comprises 48,177,783 bp with 18 scaffolds.
Fusion pore regulation by cAMP/Epac2 controls cargo release during insulin exocytosis

Regulated exocytosis establishes a narrow fusion pore as initial aqueous connection to the extracellular space, through which small transmitter molecules such as ATP can exit. Co-release of polypeptides and hormones like insulin requires further expansion of the pore. There is evidence that pore expansion is regulated and can fail in diabetes and neurodegenerative disease. Here, we report that the cAMP-sensor Epac2 (Rap-GEF4) controls fusion pore behavior by acutely recruiting two pore-restricting proteins, amisyn and dynamin-1, to the exocytosis site in insulin-secreting beta-cells. cAMP elevation restricts and slows fusion pore expansion and peptide release, but not when Epac2 is inactivated pharmacologically or in Epac2-/- (Rapgef4-/-) mice. Consistently, overexpression of Epac2 impedes pore expansion. Widely used antidiabetic drugs (GLP-1 receptor agonists and sulfonylureas) activate this pathway and thereby paradoxically restrict hormone release. We conclude that Epac2/cAMP controls fusion pore expansion and thus the balance of hormone and transmitter release during insulin granule exocytosis.
Antimicrobial and antiplasmodial activities of a quaternary compound from Ritchiea capparoides var. longipedicellata.

UNLABELLED The leaves of Ritchiea capparoides var. longipedicellata (Capparidaceae) is used in ethnomedicine in South-Western Nigeria to treat infectious and parasitic diseases. This study was aimed at identifying the compound(s) that are responsible for the antimicrobial and antiplasmodial activities of the leaves and also to contribute to the chemistry of the plant species. A 70 % aqueous ethanolic extract of the leaves of R. longipedicellata was subjected to repeated liquid chromatographic methods on silica gel, Lobar RP-18 column and Sephadex LH-20 to isolate a Draggendorf positive compound. The compound was identified by (1)H and (13)C NMR, ultra-violet spectroscopy and polarimetry. The antimicrobial activity of the compound was evaluated using the microbroth dilution method while the antiplasmodial activity was carried out according to Trager and Jenson (1976). The minimum inhibitory concentration (MIC) was expressed in mg/ml. The isolated compound, leavoisomer of stachydrine, inhibited the growth of Escherichia coli NCTC 8196 and Staphylococcus aureus NCTC 6571 at the MIC of 5 mg/ml. In the anti-malaria assay, the compound had inhibitory activity with the concentration required to cause 100% lethality being 0.667 mg/ml. CONCLUSION The antibacterial and antiparasitic effects of quaternary ammonium compounds are well documented. However, this study is the first report of the presence and biological activities of this compound in this plant species which may justify the ethnomedicinal uses of the leaves.
Radiation exposure of patients during mini C-arm use: an audit in 2032 procedures

This study aimed to audit large quantities of mini C-arm data used in hand and wrist surgery and to analyse what effect the type and anatomical location of procedures had on screening time and dose area product. Of a total of 2032 procedures, the median screening time was 11 seconds and median dose area product was 0.75 cGycm2. The third quartile value for screening time was 23 seconds and dose area product was 1.62 cGycm2. The median screening time for closed procedures was 7 seconds and the dose area product was 0.57 cGycm2. The median screening time for open surgery was 23 seconds with a median dose area product of 1.45 cGycm2. The data for steroid injection procedures were similar to those of the closed procedures, with a median screening time of 7 seconds and dose area product of 0.45 cGycm2. We found no significant differences in the screening time or dose area product between procedures on the wrist and forearm compared with the hand and digits. Level of evidence: III
Maize biology: From functional genomics to breeding application.

Maize (Zea mays L.) is one of the most important crops globally for food, feed, and fuel. Maize grain production has increased more than eight-fold in the past century to a current annual global production of one billion tons (http://faostat.fao.org/). By 2050, it will require 70% more food than today's consummation since the population size will increase to 9 billions. This article is protected by copyright. All rights reserved.
Percutaneous osteoplasty for the management of a humeral head metastasis

Rationale: Percutaneous osteoplasty (POP) has been proved effective to relieve pain in metastases of vertebral, pelvis, and femur. Nevertheless, there are few reports about the effectiveness of POP in the humeral head metastases. In this study, we described 2 patients with humeral head metastases treated with POP in our hospital. Patient concerns: Case 1 was a 79-year-old man with vertebral and right humeral head metastasis after radical surgery or and periods of chemotherapy for bladder cancer. He suffered constant severe back and right shoulder joint pain even if taking much non-steroidal anti-inflammatory drugs. Case 2 was a 59-year-old woman with vertebral and right humeral head metastasis from lung cancer. She received regular radiotherapy and took much painkillers to relieve pain. However, the pain could not be relieved any more after 1 month and severely affects sleeping and daily activities. Diagnosis: Both 2 patients were diagnosed as vertebral metastases and right proximal humeral head metastases. Interventions: POP was performed to treat the right humeral head metastases. Percutaneous vertebroplasty (PVP) was performed to treat vertebral metastases. Outcomes: After surgery, the patients experienced significant decrease in pain and better motor function. Both patients did not suffer from pulmonary embolism, infection, nerve injury, and bone cement syndrome. Lessons: For the pain that cannot be relieved by radiotherapy and analgesic drugs, POP is a safe and beneficial minimally invasive procedure that provides immediate and substantial relief from pain for humerus head metastases.
Feedback modulation of endothelial cells promotes epithelial‐mesenchymal transition and metastasis of osteosarcoma cells by Von Willebrand Factor release

Endothelial cells (ECs), as a tumor niche cell, generate and secrete Von Willebrand factor (VWF) that is linked to osteosarcoma (OS) progression. However, the role and regulatory mechanisms of VWF that underpin OS progression remain unclear. Here, using a coculture system ex vivo, we showed that ECs promoted the epithelial‐mesenchymal transition (EMT) process in OS cells via enhanced VWF secretion. VWF secreted by ECs directly contributed to OS EMT and metastasis by activating NF‐κB signaling. In addition, OS cells exerted a feedback effect on ECs to promote VWF release via activation of phospholipase D 1 signaling, through which enhanced VWF secretion results in further tumor deterioration. To conclude, ECs served as a modulator and an effector of OS, accelerating OS exacerbation by VWF release.
Exposure to outdoor air pollution and its human health outcomes: A scoping review

Despite considerable air pollution prevention and control measures that have been put into practice in recent years, outdoor air pollution remains one of the most important risk factors for health outcomes. To identify the potential research gaps, we conducted a scoping review focused on health outcomes affected by outdoor air pollution across the broad research area. Of the 5759 potentially relevant studies, 799 were included in the final analysis. The included studies showed an increasing publication trend from 1992 to 2008, and most of the studies were conducted in Asia, Europe, and North America. Among the eight categorized health outcomes, asthma (category: respiratory diseases) and mortality (category: health records) were the most common ones. Adverse health outcomes involving respiratory diseases among children accounted for the largest group. Out of the total included studies, 95.2% reported at least one statistically positive result, and only 0.4% showed ambiguous results. Based on our study, we suggest that the time frame of the included studies, their disease definitions, and the measurement of personal exposure to outdoor air pollution should be taken into consideration in any future research. The main limitation of this study is its potential language bias, since only English publications were included. In conclusion, this scoping review provides researchers and policy decision makers with evidence taken from multiple disciplines to show the increasing prevalence of outdoor air pollution and its adverse effects on health outcomes.
LSTM-Based End-to-End Framework for Biomedical Event Extraction

Biomedical event extraction plays an important role in the extraction of biological information from large-scale scientific publications. However, most state-of-the-art systems separate this task into several steps, which leads to cascading errors. In addition, it is complicated to generate features from syntactic and dependency analysis separately. Therefore, in this paper, we propose an end-to-end model based on long short-term memory (LSTM) to optimize biomedical event extraction. Experimental results demonstrate that our approach improves the performance of biomedical event extraction. We achieve average F1-scores of 59.68, 58.23, and 57.39 percent on the BioNLP09, BioNLP11, and BioNLP13's Genia event datasets, respectively. The experimental study has shown our proposed model's potential in biomedical event extraction.
Morphological and Biological Characteristics of Staphylococcus aureus Biofilm Formed in the Presence of Plasma

Characteristics of Staphylococcus aureus infections include biofilm formation, leading to the spread of bacteria to the bloodstream causing sepsis and metastatic infections. In particular, in methicillin-resistant S. aureus (MRSA) infections, biofilm formation critically hampers treatment and causes poor prognosis. We explored the biofilm formation of MRSA in the presence or absence of plasma and compared morphological characteristics, accumulation of antibiotics, and resistance to bactericidal activity, using continuous optimizing confocal reflection microscopy. Addition of plasma significantly increased biofilm formation, which is characterized by an uneven surface and aggregation of bacteria (hereafter plasma biofilm). The flow-cell system, which enabled a continuous supply of plasma, accelerated biofilm formation in both the tested strains of MRSA (BAA1556 and N315). Accumulation of green fluorescence-labeled vancomycin was observed within 5 minutes in the plasma-free biofilm, but not in the plasma biofilm. Delay of accumulation was also observed for daptomycin in plasma biofilm. Plasma biofilm bacteria were more resistant to anti-MRSA antibiotics than plasma-free biofilm bacteria. These data demonstrate that the plasma biofilm of S. aureus is substantially different from the plasma-free biofilm. Plasma biofilm, especially in the flow-cell system, could be a clinically relevant model to analyze MRSA infections and treatment.
Food insecurity, childhood hunger and caregiver life experiences among households with children in South Carolina, USA

Abstract Objective: We explored how positive and negative life experiences of caregivers are associated with household food insecurity. Design: The Midlands Family Study (MFS) was a cross-sectional study with three levels of household food security: food secure, food insecure without child hunger and food insecure with child hunger. Ordinal logistic regression analysis was used for analyses of negative and positive life experiences (number, impact, type) associated with food insecurity. Setting: An eight-county region in South Carolina, USA, in 2012–2013. Participants: Caregivers (n 511) in households with children. Results: Caregivers who reported greater numbers of negative life experiences and greater perceived impact had increased odds of household food insecurity and reporting their children experienced hunger. Each additional negative life experience count of the caregiver was associated with a 16 % greater odds of food insecurity without child hunger and a 28 % greater odds of child hunger. Each one-unit increase in the negative impact score (e.g. a worsening) was associated with 8 % higher odds of food insecurity without child hunger and 12 % higher odds of child hunger. Negative work experiences or financial instability had the strongest association (OR = 1·8; 95 % CI 1·5, 2·2) with child hunger. Positive life experiences were generally not associated with food security status, with one exception: for each unit increase in the number of positive experiences involving family and other relationships, the odds of child hunger decreased by 22 %. Conclusions: More research is needed to understand approaches to build resilience against negative life experiences and strengthen positive familial, community and social relationships.
Association between etiologic factors in infertile couples and fertilization failure in conventional in vitro fertilization cycles

The aim of this study was to investigate the relationship between the etiology of the couples and risk of fertilization failure (FF) in conventional in vitro fertilization (IVF) cycles and the effect of rescue intracytoplasmic sperm injection (ICSI) technique to offspring. A total of 2542 IVF cycles were divided into four groups according to infertile etiology: Group A – primary infertility with normal semen parameters; Group B – secondary infertility with oligoasthenozoospermia; Group C – primary infertility with oligoasthenozoospermia; and Group D – secondary infertility with normal semen parameters. The results showed that there were significant differences in incidence of FF among Group A (16.8%), Group B (20.9%), Group C (48.7%), and Group D (0.9%) (p < 0.001). Logistic regression models demonstrated that primary infertility (OR: 10.898, 95% CI: 4.651–25.583, p < 0.001) and oligoasthenozoospermia (OR: 12.215, 95% CI: 5.903–25.276, p < 0.001) were independent risk factors for FF. There were no significant differences in main outcomes between conventional ICSI and rescue ICSI. In conclusion, the patients with primary infertility and oligoasthenozoospermia might be at higher risk of FF. The rescue ICSI technique is safe and helpful for IVF cycles of FF.
Low-intensity exercise induces acute shifts in liver and skeletal muscle substrate metabolism, but not chronic adaptations in tissue oxidative capacity.

Adaptations in hepatic and skeletal muscle substrate metabolism following acute and chronic (6 weeks; 5 days/week; 1 h/day) low-intensity treadmill exercise were tested in healthy male C57BL/6J mice. Low-intensity exercise maximizes lipid utilization; therefore, we hypothesized pathways involved in lipid metabolism would be most robustly affected. Acute exercise nearly depleted liver glycogen immediately post-exercise (0h), while hepatic triglyceride (TAG) stores increased in the early stages after exercise (0-3h). Also, hepatic Pgc-1a gene expression and fat oxidation (mitochondrial and peroxisomal) increased immediately post-exercise (0h), whereas carbohydrate and amino acid oxidation in liver peaked 24-48h later. Alternatively, skeletal muscle exhibited a less robust response to acute exercise as stored substrates (glycogen and TAG) remained unchanged, induction of Pgc-1a gene expression was delayed (up at 3h), and mitochondrial substrate oxidation pathways (carbohydrate, amino acid and lipid) were largely unaltered. Peroxisomal lipid oxidation exhibited the most dynamic changes in skeletal muscle substrate metabolism after acute exercise; however, this response was also delayed (peaked 3-24h post-exercise) and expression of peroxisomal genes remained unaffected. Interestingly, 6 weeks of training at a similar intensity limited weight gain, increased muscle glycogen, and reduced TAG accrual in liver and muscle; however, substrate oxidation pathways remained unaltered in both tissues. Collectively these results suggest changes in substrate metabolism induced by an acute low-intensity exercise bout in healthy mice are more rapid and robust in liver than in skeletal muscle; however, training at a similar intensity for 6 weeks is insufficient to induce remodeling of substrate metabolism pathways in either tissue.
Natural history of Homo erectus.

Our view of H. erectus is vastly different today than when Pithecanthropus erectus was described in 1894. Since its synonimization into Homo, views of the species and its distribution have varied from a single, widely dispersed, polytypic species ultimately ancestral to all later Homo, to a derived, regional isolate ultimately marginal to later hominin evolution. A revised chronostratigraphic framework and recent work bearing either directly or indirectly on reconstructions of life-history patterns are reviewed here and, together with a review of the cranial and postcranial anatomy of H. erectus, are used to generate a natural history of the species. Here I argue that H. erectus is a hominin, notable for its increased body size, that originates in the latest Pliocene/earliest Pleistocene of Africa and quickly disperses into Western and Eastern Asia. It is also an increasingly derived hominin with several regional morphs sustained by intermittent isolation, particularly in Southeast Asia. This view differs from several current views, most especially that which recognizes only a single hominin species in the Pleistocene, H. sapiens, and those which would atomize H. erectus into a multiplicity of taxa. Following Jolly ([2001] Yrbk Phys Anthropol 44:177-204), the regional morphs of H. erectus may be productively viewed as geographically replacing allotaxa, rather than as the focus of unresolvable species debates. Such a view allows us to focus on the adaptations and biology of local groups, including questions of biogeographic isolation and local adaptation. A number of issues remain unresolved, including the significance of diversity in size and shape in the early African and Georgian records.