Miracle-dz/UniFAR-FTUs huggingface dataset:
ATTED-II provides coexpressed gene networks for Arabidopsis

ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein–protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis.
Seroprevalence and Severity of 2009 Pandemic Influenza A H1N1 in Taiwan

Background This study is to determine the seroprevalence of the pandemic influenza A H1N1 virus (pH1N1) in Taiwan before and after the 2009 pandemic, and to estimate the relative severity of pH1N1 infections among different age groups. Methodology/Principal Findings A total of 1544 and 1558 random serum samples were collected from the general population in Taiwan in 2007 and 2010, respectively. Seropositivity was defined by a hemagglutination inhibition titer to pH1N1 (A/Taiwan/126/09) ≥1:40. The seropositivity rate of pH1N1 among the unvaccinated subjects and national surveillance data were used to compare the proportion of infections that led to severe diseases and fatalities among different age groups. The overall seroprevalence of pH1N1 was 0.91% (95% confidence interval [CI] 0.43–1.38) in 2007 and significantly increased to 29.9% (95% CI 27.6–32.2) in 2010 (p<0.0001), with the peak attack rate (55.4%) in 10–17 year-old adolescents, the lowest in elderly ≥65 years (14.1%). The overall attack rates were 20.6% (188/912) in unvaccinated subjects. Among the unvaccinated but infected populations, the estimated attack rates of severe cases per 100,000 infections were significantly higher in children aged 0–5 years (54.9 cases, odds ratio [OR] 4.23, 95% CI 3.04–5.90) and elderly ≥ 65years (22.4 cases, OR 2.76, 95% CI 1.99–3.83) compared to adolescents aged 10–17 years (13.0 cases). The overall case-fatality rate was 0.98 per 100,000 infections without a significant difference in different age groups. Conclusions/Significance Pre-existing immunity against pH1N1 was rarely identified in Taiwanese at any age in 2007. Young children and elderly – the two most lower seroprotection groups showed the greatest vulnerability to clinical severity after the pH1N1 infections. These results imply that both age groups should have higher priority for immunization in the coming flu season.
Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells

Several reports suggest that CmCWGG methylation tends not to co-exist with mCG methylation in human cells. We have asked whether or not methylation at CCWGG sites can influence CG methylation. DNA from cells expressing an M.EcoRII–GFP fusion was actively methylated at CCWGG sites. CG methylation as measured by R.HpaII/R.MspI ratios was unchanged in cells expressing the transgene. Cloned representatives of CmCWGG methylated DNA often contained, or were adjacent to an ALU repeat, suggesting that M.EcoRII-GFP actively methylated gene-rich R-band DNA. The transgenic methyltransferase applied CmCWGG methylation to a representative human promoter that was heavily methylated at CG dinucleotides (the SERPINB5 promoter) and to a representative promoter that was essentially unmethylated at CG dinucleotides (the APC promoter). In each case, the CG methylation pattern remained in its original state, unchanged by the presence of neighboring CmCWGG sites. Q-PCR measurements showed that RNA expression from the APC gene was not significantly altered by the presence of CmCWGG in its promoter. Kinetic studies suggested that an adjacent CmCWGG methylation site influences neither the maintenance nor the de novo methylation activities of purified human Dnmt1. We conclude that CmCWGG methylation does not exert a significant effect on CG methylation in human kidney cells.
Aging influences steroid hormone release by mink ovaries and their response to leptin and IGF-I

ABSTRACT The aim of our study was to understand whether ovarian steroid hormones, and their response to the metabolic hormones leptin and IGF-I leptin, could be involved in the control of mink reproductive aging via changes in basal release of ovarian progesterone and estradiol. For this purpose, we compared the release of progesterone and estradiol by ovarian fragments isolated from young (yearlings) and old (3-5 years of age) minks cultured with and without leptin and IGF-I (0, 1, 10 or 100 ng/ml). We observed that isolated ovaries of older animals produced less progesterone but not less estradiol than the ovaries of young animals. Leptin addition stimulated estradiol release by the ovarian tissue of young animals but inhibited it in older females. Leptin did not influence progesterone output by the ovaries of either young or older animals. IGF-I inhibited estradiol output in young but not old animals, whereas progesterone release was inhibited by IGF-I irrespective of the animal age. Our observations demonstrate the involvement of both leptin and IGF-I in the control of mink ovarian steroid hormones release. Furthermore, our findings suggest that reproductive aging in minks can be due to (a) reduction in basal progesterone release and (b) alterations in the response of estradiol but not of progesterone to leptin and IGF-I. Summary: Both leptin and IGF-I are involved in the control of mink ovarian steroid hormone release. Reproductive aging can be due to (a) reduction in basal progesterone release and (b) alterations in the response of estradiol but not of progesterone to leptin and IGF-I.
Object Detection in RGB-D Indoor Scenes 1

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission. Acknowledgement I'd like to thank my advisor, Jitendra Malik, for being an invaluable source of wisdom and direction in my thesis project, and for supporting my time in the vision lab. I'd also like to thank Ross Girshick and Saurabh Gupta for their immeasurable help. for their substantial guidance along the way. Finally, and perhaps most importantly, I'd like to thank my family and friends. Y'all made it worthwhile.
Genome-wide analysis of Musashi-2 targets reveals novel functions in governing epithelial cell migration

The Musashi-2 (Msi2) RNA-binding protein maintains stem cell self-renewal and promotes oncogenesis by enhancing cell proliferation in hematopoietic and gastrointestinal tissues. However, it is unclear how Msi2 recognizes and regulates mRNA targets in vivo and whether Msi2 primarily controls cell growth in all cell types. Here we identified Msi2 targets with HITS-CLIP and revealed that Msi2 primarily recognizes mRNA 3′UTRs at sites enriched in multiple copies of UAG motifs in epithelial progenitor cells. RNA-seq and ribosome profiling demonstrated that Msi2 promotes targeted mRNA decay without affecting translation efficiency. Unexpectedly, the most prominent Msi2 targets identified are key regulators that govern cell motility with a high enrichment in focal adhesion and extracellular matrix-receptor interaction, in addition to regulators of cell growth and survival. Loss of Msi2 stimulates epithelial cell migration, increases the number of focal adhesions and also compromises cell growth. These findings provide new insights into the molecular mechanisms of Msi2's recognition and repression of targets and uncover a key function of Msi2 in restricting epithelial cell migration.
Real-Time Amperometric Recording of Extracellular H2O2 in the Brain of Immunocompromised Mice: An In Vitro, Ex Vivo and In Vivo Characterisation Study

We detail an extensive characterisation study on a previously described dual amperometric H2O2 biosensor consisting of H2O2 detection (blank) and degradation (catalase) electrodes. In vitro investigations demonstrated excellent H2O2 sensitivity and selectivity against the interferent, ascorbic acid. Ex vivo studies were performed to mimic physiological conditions prior to in vivo deployment. Exposure to brain tissue homogenate identified reliable sensitivity and selectivity recordings up to seven days for both blank and catalase electrodes. Furthermore, there was no compromise in pre- and post-implanted catalase electrode sensitivity in ex vivo mouse brain. In vivo investigations performed in anaesthetised mice confirmed the ability of the H2O2 biosensor to detect increases in amperometric current following locally perfused/infused H2O2 and antioxidant inhibitors mercaptosuccinic acid and sodium azide. Subsequent recordings in freely moving mice identified negligible effects of control saline and sodium ascorbate interference injections on amperometric H2O2 current. Furthermore, the stability of the amperometric current was confirmed over a five-day period and analysis of 24-h signal recordings identified the absence of diurnal variations in amperometric current. Collectively, these findings confirm the biosensor current responds in vivo to increasing exogenous and endogenous H2O2 and tentatively supports measurement of H2O2 dynamics in freely moving NOD SCID mice.
Hypertension in the Elderly

Background. The incidence of hypertension in the Western countries is continuously increasing in the elderly population and remains the leading cause of cardiovascular and morbidity. Methods. we analysed some significant clinical trials in order to present the relevant findings on those hypertensive population. Results. Several studies (SYST-EUR, HYVET, CONVINCE, VALUE, etc.) have demonstrated the benefits of treatment (nitrendipine, hydrochrotiazyde, perindopril, indapamide, verapamil, or valsartan) in aged hypertensive patients not only concerning blood pressure values but also the other important risk factors. Conclusion. Hypertension is the most prevalent cardiovascular disorder in the Western countries, and the relevance of receiving pharmacological treatment of hypertension in aged patients is crucial; in addition, the results suggest that combination therapy—nitrendipine plus enalapril—could have more benefits than those observed with the use of nitrendipine alone.
Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa

Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene–gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.
Accurately Estimating Sherd 3D Surface Geometry with Application to Pot Reconstruction

This paper deals with the problem of precise automatic estimation of the surface geometry of pot sherds uncovered at archaeological excavation sites using dense 3D laser-scan data. Critical to ceramic fragment analysis is the ability to geometrically classify excavated sherds, and, if possible, reconstruct the original pots using the sherd fragments. To do this, archaelogists must estimate the pot geometry in terms of an axis and associated profile curve from the discovered fragments. In this paper, we discuss an automatic method for accurately estimating an axis/profile curve pair for each archeological sherd (even when they are small) based on axially symmetric implicit polynomial surface models. Our method estimates the axis/profile curve for a sherd by finding the axially symmetric algebraic surface which best fits the measured set of dense 3D points and associated normals. We note that this method will work on 3D point data alone and does not require any local surface computations such as differentiation. Axis/profile curve estimates are accompanied by a detailed statistical error analysis. Estimation and error analysis are illustrated with application to a number of sherds. These fragments, excavated from Petra, Jordan, are chosen as exemplars of the families of geometrically diverse sherds commonly found on an archeological excavation site. We then briefly discuss how the estimation results may be integrated into a larger pot reconstruction program.
Role of 18F-fluorodeoxyglucose Positron Emission Tomography scan in differentiating enhancing brain tumors

Aim: To determine whether F-18-fluorodeoxyglucose positron emission tomography (F-18-FDG PET) can be used to differentiate among common enhancing brain tumors such as gliomas, metastatic brain tumors, and lymphoma. Materials and Methods: We evaluated 20 patients with an enhancing brain tumor on magnetic resonance imaging (MRI). FDG PET scan was done in all patients pre operatively. For PET image analysis, regions of interest were placed over the tumor (T), contralateral cortex (C), and white matter (WM). Average and maximum pixel values were determined at each site. On the basis of these measurements, average and maximum standard uptake values (SUV avg and SUV max ) were calculated, and comparisons among lesions were then made. Results: SUVavg and SUVmax are significantly higher for central nervous system (CNS) lymphoma than for other tumors (P < 0.01). High-grade gliomas showed significantly higher SUVavg and SUVmax than the low grade gliomas (P < 0.05) and metastatic tumor showed higher SUVavg and SUVmax than all gliomas, both low and high grade (P < 0.05). When the lowest values of CNS lymphoma parameter were used as cutoff levels to distinguish CNS lymphomas from other tumors (i.e. 100% sensitivity), SUVmax was the most accurate parameter. Using a SUVmax of 15.0 as a cutoff for diagnosing CNS lymphoma, only one case of metastasis (SUV max , 16.3) was found to be false positive in this study. Conclusion: FDG PET appears to provide additional information for differentiating common enhancing malignant brain tumors, namely lymphoma versus high grade glioma and metastatic tumor, particularly when differential diagnoses are difficult to narrow using MRI alone.
Cerebral blood flow velocity changes during upright positioning in bed after acute stroke: an observational study

Objectives National guidelines recommend mobilisation in bed as early as possible after acute stroke. Little is known about the influence of upright positioning on real-time cerebral flow variables in patients with stroke. We aimed to assess whether cerebral blood flow velocity (CBFV) changes significantly after upright positioning in bed in the acute stroke phase. Design Observational study. Participants 47 patients with acute ischaemic stroke measured in the subacute phase after symptom onset and 20 healthy controls. Primary and secondary outcome measures We recorded postural changes in bilateral transcranial Doppler (primary outcome) and simultaneously recorded near-infrared spectroscopy, end-tidal CO2, non-invasive blood pressure data and changes in neurological status (secondary outcomes). Methods Postures included the supine, half sitting (45°), sitting (70°) and Trendelenburg (−15°) positions. Using multilevel analyses, we compared postural changes between hemispheres, outcome groups (using modified Rankin Scale) as well as between patients and healthy controls. Results The mean patient age was 62±15 years and median National Institute of Health Stroke Scale score on admission was 7 (IQR 5–14). Mean proportional CBFV changes on sitting were not significantly different between healthy controls and affected hemispheres in patients with stroke. No significant differences were found between affected and unaffected stroke hemispheres and between patients with unfavourable and favourable outcomes. During upright positioning, no neurological worsening or improvement was observed in any of the patients. Conclusions No indications were found that upright positioning in bed in mild to moderately affected patients with stroke compromises flow and (frontal)oxygenation significantly during the subacute phase of stroke. Supine or Trendelenburg positioning does not seem to augment real-time flow variables.
Long-term sickness absence among patients with chronic fatigue syndrome

Summary Chronic fatigue syndrome is associated with high levels of occupational disability. Consecutive out-patients at a chronic fatigue syndrome treatment service were studied for associations between occupational status, symptom severity and cognitive and behavioural responses to symptoms. All patients had high symptom levels; however, those on long-term sickness absence had significantly more physical fatigue (β = 0.098, P<0.05) and worse sleep (β = 0.075, P<0.05). Patients with long-term sickness absence also demonstrated more embarrassment avoidance cognitions (β = 0.086, P<0.05) and avoidance resting behavioural responses (β = 0.078, P<0.05). Identifying and addressing avoidance behaviours and cognitions regarding embarrassment in interventions may enhance the chances of individuals returning to work.
Non-cholinergic drug development for Alzheimer's disease

Background: Recent advances in the understanding of the pathobiology of Alzheimer's disease have led to a large number of non-cholinergic targets for the development of therapeutic agents. These include, for example, neurotransmitter-based, anti-amyloid, antitangle, antioxidant, anti-excitotoxic, and growth factor strategies. There are several hundred agents in, or approaching, clinical trials. Some hold promise for treatment of those affected, some may have potential for prevention, some for both. Objectives: Key examples of each of these development approaches will be summarized. Conclusions: It is too soon to predict which, if any, of these approaches will bear fruit. At the moment, it appears that the amyloid-based therapies are the farthest along in development, and have shown in some cases that the amyloid dysregulation cascade can be interrupted. It is unknown, however, whether altering this aspect of the pathobiology of Alzheimer's will actually yield clinical benefit. Efforts to affect tangle development would appear to be a fruitful approach, although these efforts lag behind the anti-amyloid efforts. The same is essentially true for the other approaches reviewed as well. Given the fact that many new interventions target specific pathways that can be measured biologically in go–no go proof of concept studies, the opportunity exists to capitalize on biomarkers in earlier stages of development. The same can be said for evolving imaging techniques. Given the number of agents in development, we offer the provocative suggestion that the biggest threat to identifying effective therapies may prove to be the implementation of enough treatment trials, and applying out-of-the-box prevention methodologies, rather than the discovery of promising candidates. This prediction may or may not hold true.
Decreased synaptic proteins in neuronal exosomes of frontotemporal dementia and Alzheimer's disease

Synaptic dysfunction occurs early in senile dementias, presumably as a result of decreased levels of functional synaptic proteins as found in autopsied brains of patients with Alzheimer's disease (AD) or frontotemporal dementia (FTD). Plasma neuronal‐derived exosomes (NDEs) were recovered by precipitation and immunoabsorption from 12 patients with AD, 16 with FTD, and 28 controls in a cross‐sectional study, and from 9 patients with AD, 10with FTD, and 19 controls in a longitudinal study. Six synaptic proteins in NDE extracts were quantified by ELISAs and normalized for exosome amounts. NDE levels of synaptophysin, synaptopodin, synaptotagmin‐2, and neurogranin were significantly lower in patients with FTD and ADthan in controls, but those of growth‐associated protein 43 and synapsin 1 were reduced only in patients with AD. Functionally relevant phosphorylation of synapsin 1 serine 9 was reduced in patients with FTD and AD, although total synapsin 1 protein was higher in FTD than in controls. NDE levels of synaptotagmin, synaptophysin, and neurograninwere decreased yearsbeforedementia inpatientswithFTD and AD.NDElevelsof synaptopodin, synaptotagmin, and synaptophysin, but not of amyloid β‐peptide 42 or P‐T181‐tau, were correlated significantly with cognition assessed bymini‐mental state examination or AD assessment scale‐cognitive subscale. NDE synaptic proteins may be useful preclinical indices and progression measures in senile dementias. —Goetzl, E. J., Kapogiannis, D. , Schwartz, J. B. , Lobach, I. V. , Goetzl, L. , Abner, E. L. , Jicha, G. A. , Karydas, A.M., Boxer, A. , Miller, B. L. Decreased synaptic proteins in neuronal exosomes of frontotemporal dementia and Alzheimer's disease. FASEB J. 30, 4141–4148 (2016). www.fasebj. org
Morphometry of dorsal root ganglion in chronic experimental diabetic neuropathy.

Chronic hyperglycemia results in a predominantly sensory neuropathy. Recent studies suggest that dorsal root ganglion (DRG) neurons comprise a specific target and may be responsible for the important complication of diabetic sensory neuropathy, since hyperglycemia for longer than 6 months results in a vacuolar ganglionopathy with associated radiculopathy and distal sensory neuropathy. We undertook morphometric analysis of L5 DRG neurons in seven diabetic rats and six age- and sex-matched littermates. Nerve conduction studies were also performed, and neuropathy was confirmed. Diabetes was induced with streptozotocin; duration of diabetes was 12 months. The DRG count for control rats was 15,304 +/- 991 neurons. Two of seven diabetic DRG counts were reduced, but the group mean count at 14,847 plus minus 1,524 was not significantly reduced. The number of small neurons (type B) considerably exceeded that of large neurons (type A), at a ratio of 71:29. The percentage of large cells was significantly reduced in diabetic compared with control rats (P = 0.01). The large-diameter population can be subdivided into two groups; with this subdivision, the number of neurons < 50 microm was not reduced in samples from diabetic rats, but the neurons of largest size (> or = 50 microm) were significantly reduced (by 41%).