Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Analysis of WRKY Genes and Their Response to Hormone and Mechanic Stresses in Carrot

The WRKY gene family plays a vital role in plant development and environment response. Although previous studies suggested that the WRKY genes in carrot (Kuroda type) involved in biotic and abiotic stress responses, the information of WRKY genes in the latest version of the carrot genome (Daucus carota v2.0, Nantes type carrot) and their response to hormone and injury stresses have not been reported. In this study, we performed a genome-wide analysis of WRKYs using a chromosome-scale genome assembly of carrot (Daucus carota subsp. sativus L.). We identified a total of 67 WRKY genes, which were further classified into the three groups. These WRKY genes are unevenly distributed on carrot chromosomes. We found that more than half of them were derived from whole-genome duplication (WGD) events, suggesting that WGDs have played a major role during the evolution of the WRKY gene family. We experimentally ascertained the expression divergence existed between WGD-derived WRKY duplicated gene pairs, which is indicative of functional differentiation between duplicated genes. Our analysis of cis-acting elements indicated that WRKY genes were transcriptionally regulated upon hormone and mechanic injury stresses. Gene expression analyses by qRT-PCR further presented that WRKY genes were involved in hormone and mechanic injury stresses.
THE EFFECTS OF PREDATION RISK ON MATING SYSTEM EXPRESSION IN A FRESHWATER SNAIL

Environmental effects on mating system expression are central to understanding mating system evolution in nature. Here, I report the results from a quantitative‐genetic experiment aimed at understanding the role of predation risk in the expression and evolution of life‐history and mating‐system traits in a hermaphroditic freshwater snail (Physa acuta). I reared 30 full‐sib families in four environments that factorially contrast predation risk and mate availability and measured age/size at first reproduction, growth rate, a morphological defense, and the early survival of outcrossed/selfed eggs that were laid under predator/no‐predator conditions. I evaluated the genetic basis of trade‐offs among traits and the stability of the G matrix across environments. Mating reduced growth while predation risk increased growth, but the effects of mating were weaker for predator‐induced snails and the effects of predation risk were weaker for snails without mates. Predation risk reduced the amount of time that individuals waited before self‐fertilizing and reduced inbreeding depression in the offspring. There was a positive among‐family relationship between the amount of time that individuals delayed selfing under predation risk and the magnitude of inbreeding depression. These results highlight several potential roles of enemies in mating‐system expression and evolution.
Lateral Hypothalamic Projections to the Rat Ventral Tegmental Area: Potential Anatomical Substrates for Adaptive Integration of Behaviors Mediated by Ascending Dopamine Systems

Complex motor behaviors enable mammals to adapt to their internal and external environments. The lateral hypothalamic area (LHA) contributes importantly to autonomic and endocrine regulation, behavioral states, and energy balance. Orexin (Orx) neuropeptides, produced exclusively by LHA cells, are crucial in the integration of sleep and arousal. The LHA projects densely to the ventral tegmental area (VTA), a dopamine (DA) region that is essential for modulating goal-directed behaviors. Extensive investigations of reward function implicate the LHA-VTA connectivity, an arrangement not yet characterized in detail at the ultrastructural level. The present research sought to clarify the precise interactions of LHA axons with VTA cells. Considering reported physiological responses of VTA cells to LHA stimulation and Orx actions, we hypothesized that both projections interact heavily with DA and GABA cell groups in the VTA, and that LHA axons provide a predominant inhibitory innervation. We used immunocytochemistry to visualize DA or GABA neurons in combination with 1) tract tracer identification of LHA axons or 2) immunolabeling for Orx. Electron microscopic analysis of the VTA revealed that, while the bulk of LHA and Orx projections pass through the VTA, their connections with DA and GABA neurons are a complementary mixture of excitatory and inhibitory synapses. The details of morphology herein suggest many different mechanisms of signal transmission by which LHA axons might contribute information concerning interoceptive state to the adaptive performance of complex motor behaviors modulated by the VTA.
Fluctuations in isometric muscle force can be described by one linear projection of low‐frequency components of motor unit discharge rates

The aim of the study was to investigate the relation between linear transformations of motor unit discharge rates and muscle force. Intramuscular (wire electrodes) and high‐density surface EMG (13 × 5 electrode grid) were recorded from the abductor digiti minimi muscle of eight healthy men during 60 s contractions at 5%, 7.5% and 10% of the maximal force. Spike trains of a total of 222 motor units were identified from the EMG recordings with decomposition algorithms. Principal component analysis of the smoothed motor unit discharge rates indicated that one component (first common component, FCC) described 44.2 ± 7.5% of the total variability of the smoothed discharge rates when computed over the entire contraction interval and 64.3 ± 10.2% of the variability when computed over 5 s intervals. When the FCC was computed from four or more motor units per contraction, it correlated with the force produced by the muscle (62.7 ± 10.1%) by a greater degree (P < 0.001) than the smoothed discharge rates of individual motor units (41.4 ± 7.8%). The correlation between FCC and the force signal increased up to 71.8 ± 13.1% when the duration and the shape of the smoothing window for discharge rates were similar to the average motor unit twitch force. Moreover, the coefficients of variation (CoV) for the force and for the FCC signal were correlated in all subjects (R2 range = 0.14–0.56; P < 0.05) whereas the CoV for force was correlated to the interspike interval variability in only one subject (R2= 0.12; P < 0.05). Similar results were further obtained from measures on the tibialis anterior muscle of an additional eight subjects during contractions at forces up to 20% of the maximal force (e.g. FCC explained 59.8 ± 11.0% of variability of the smoothed discharge rates). In conclusion, one signal captures most of the underlying variability of the low‐frequency components of motor unit discharge rates and explains large part of the fluctuations in the motor output during isometric contractions.
The effect of age on pain, function, and quality of life after total hip and knee arthroplasty.

BACKGROUND As utilization rates for total joint arthroplasty increase, there is a hesitancy to perform this surgery on very old patients. The objective of this prospective study was to compare pain, functional, and health-related quality-of-life outcomes after total hip and total knee arthroplasty in an older patient group (> or =80 years) and a representative younger patient group (55-79 years). METHODS In an inception community-based cohort within a Canadian health care system, 454 patients who received primary total hip arthroplasty (n = 197) or total knee arthroplasty (n = 257) were evaluated within a month prior to surgery and 6 months postoperatively. Pain, function, and health-related quality of life were evaluated with the Western Ontario and McMaster Universities (WOMAC) Osteoarthritis Index and the 36-Item Short-Form Health Survey (SF-36). RESULTS There were no age-related differences in joint pain, function, or quality-of-life measures preoperatively or 6 months postoperatively. Furthermore, after adjusting for potential confounding effects, age was not a significant determinant of pain or function. Although those in the older and younger groups had comparable numbers of comorbid conditions and complications, those in the older group were more likely to be transferred to a rehabilitation facility than younger patients. Regardless of age, patients did not achieve comparable overall physical health when matched with the general population for age and sex. CONCLUSIONS With increasing life expectancy and elective surgery improving quality of life, age alone is not a factor that affects the outcome of joint arthroplasty and should not be a limiting factor when considering who should receive this surgery.
Influenza vaccination of pregnant women and protection of their infants.

BACKGROUND There are limited data on the efficacy of vaccination against confirmed influenza in pregnant women with and those without human immunodeficiency virus (HIV) infection and protection of their infants. METHODS We conducted two double-blind, randomized, placebo-controlled trials of trivalent inactivated influenza vaccine (IIV3) in South Africa during 2011 in pregnant women infected with HIV and during 2011 and 2012 in pregnant women who were not infected. The immunogenicity, safety, and efficacy of IIV3 in pregnant women and their infants were evaluated until 24 weeks after birth. Immune responses were measured with a hemagglutination inhibition (HAI) assay, and influenza was diagnosed by means of reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assays of respiratory samples. RESULTS The study cohorts included 2116 pregnant women who were not infected with HIV and 194 pregnant women who were infected with HIV. At 1 month after vaccination, seroconversion rates and the proportion of participants with HAI titers of 1:40 or more were higher among IIV3 recipients than among placebo recipients in both cohorts. Newborns of IIV3 recipients also had higher HAI titers than newborns of placebo recipients. The attack rate for RT-PCR-confirmed influenza among both HIV-uninfected placebo recipients and their infants was 3.6%. The attack rates among HIV-uninfected IIV3 recipients and their infants were 1.8% and 1.9%, respectively, and the respective vaccine-efficacy rates were 50.4% (95% confidence interval [CI], 14.5 to 71.2) and 48.8% (95% CI, 11.6 to 70.4). Among HIV-infected women, the attack rate for placebo recipients was 17.0% and the rate for IIV3 recipients was 7.0%; the vaccine-efficacy rate for these IIV3 recipients was 57.7% (95% CI, 0.2 to 82.1). CONCLUSIONS Influenza vaccine was immunogenic in HIV-uninfected and HIV-infected pregnant women and provided partial protection against confirmed influenza in both groups of women and in infants who were not exposed to HIV. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov numbers, NCT01306669 and NCT01306682.).
INTRANUCLEAR AND CYTOPLASMIC ANNULATE LAMELLAE IN PLANT CELLS

Annulate lamellae (AL) have hitherto been described for ammal cells (m particular, for germ cells), for embryomc systems, and for rapidly growing cells hke tumor and cancer ceils (for review, see references I0, 16) Such cisternae, which are either single or arranged m stacks of parallel lamellae, are characterized by the presence of pore complexes, i.e., pores of a relatively unitbrm srze distribution which are associated with distinct granulo-fibrillar structures and are arranged m a symmetrical subarchitecture identical to that of nuclear pore complexes (e g., 10, 14). No micrograph has so far been published which documents the presence of such structures in plant ceils. Kessel (10), though, in an addendum to his review, mentioned nonpublished observations of Skvarla who claimed the existence of "extensive profiles of annulate lamellae in pollen of Canna during pollen wall formation " We have been able to confirm this remark and, additionally, have found that stacks of AL occur also m earher stages of microsporogenesls (e g , pollen mother ceils) of Cannaceae and Zzngzberaceae 1 Sen (15) has demonstrated membranous stacks of Lilzurn microsporocyte metotto prophase and discussed a relationship to annulate lamellar formations, but these lamelIae do not show any pore complexes and thus are to be regarded as stacked endoplasmic ret iculum (ER) e rather than AL The question is whether AL in plant cells are confined to pollen development of a few species or are of more general occurrence Since in animal cells AL have been described mostly from cell types with a high R N A synthesis including, e g. diverse
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes

SUMMARY At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION A SPOCS web application is freely available at http://cbb.pnnl. gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl. gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.
Sun exposure and risk of melanoma

Background: As skin cancer education programmes directed to children and adolescents continue to expand, an epidemiological basis for these programmes is necessary to target efforts and plan for further evaluation. Aims: To summarise the epidemiological evidence on sun exposure during childhood and adolescence and melanoma risk. Methods: A literature review was conducted using Medline (1966 to December 2004) to identify articles relating to sun exposure and melanoma. The review was restricted to studies that included sun exposure information on subjects 18 years of age or younger. Results: Migrant studies generally indicate an increased melanoma risk in individuals who spent childhood in sunny geographical locations, and decreasing melanoma risk with older age at arrival. Individuals who resided in geographical locations close to the equator or close to the coast during childhood and/or adolescence have an increased melanoma risk compared to those who lived at higher latitudes or never lived near the coast. The intermittent exposure hypothesis remains controversial; some studies indicate that children and adolescents who received intermittent sun exposure during vacation, recreation, or occupation are at increased melanoma risk as adults, but more recent studies suggest intermittent exposure to have a protective effect. The majority of sunburn studies suggest a positive association between early age sunburn and subsequent risk of melanoma. Conclusion: Future research efforts should focus on: (1) clarifying the relation between sun exposure and melanoma; (2) conducting prospective studies; (3) assessing sun exposure during different time periods of life using a reliable and quantitative method; (4) obtaining information on protective measures; and (5) examining the interrelations between ability to tan, propensity to burn, skin type, history of sunburns, timing and pattern of sun exposure, number of nevi, and other host factors in the child and adolescent populations.
Gesture Salience as a Hidden Variable for Coreference Resolution and Keyframe Extraction

Gesture is a non-verbal modality that can contribute crucial information to the understanding of natural language. But not all gestures are informative, and noncommunicative hand motions may confuse natural language processing (NLP) and impede learning. People have little difficulty ignoring irrelevant hand movements and focusing on meaningful gestures, suggesting that an automatic system could also be trained to perform this task. However, the informativeness of a gesture is context-dependent and labeling enough data to cover all cases would be expensive. We present conditional modality fusion, a conditional hidden-variable model that learns to predict which gestures are salient for coreference resolution, the task of determining whether two noun phrases refer to the same semantic entity. Moreover, our approach uses only coreference annotations, and not annotations of gesture salience itself. We show that gesture features improve performance on coreference resolution, and that by attending only to gestures that are salient, our method achieves further significant gains. In addition, we show that the model of gesture salience learned in the context of coreference accords with human intuition, by demonstrating that gestures judged to be salient by our model can be used successfully to create multimedia keyframe summaries of video. These summaries are similar to those created by human raters, and significantly outperform summaries produced by baselines from the literature.
The Unique Phenomenology of Sex-Linked Dystonia Parkinsonism (XDP, DYT3, “Lubag”)

ABSTRACT Sex-linked dystonia parkinsonism (XDP, DYT3, “Lubag”) is an adult-onset, progressive, debilitating movement disorder first described in Filipino males from Panay Islands in 1975. XDP manifests predominantly as torsion dystonia, later combined with or sometimes replaced with parkinsonism. Within the Island of Panay, the prevalence rate is highest in the province of Capiz, where 1:4000 men suffer from the disorder. There is a high degree of penetrance and generalization. While women often serve as carriers, XDP is not limited to men. An updated XDP Philippine registry (as of January 2010) has identified 505 cases, with 500 males and 5 females. While some report that females may carry a milder form of the disorder, in our experience, both sexes generally follow a similar progressive clinical course.
Expression of Epidermal Growth Factor Receptor (EGFR) and Activated EGFR Predict Poor Response to (Chemo)radiation and Survival in Cervical Cancer

Purpose: Activation of the epidermal growth factor receptor (EGFR) signaling pathway has been reported to induce resistance to (chemo)radiation in cancers, such as head and neck cancer, whereas EGFR-targeted agents in combination with (chemo)radiation seem to improve treatment efficacy. The aim of this study was to determine the relation between proteins involved in the EGFR pathway and response to (chemo)radiation and survival in a large, well-documented series of cervical cancer patients. Experimental Design: Pretreatment tissue samples of 375 consecutive International Federation of Gynecologists and Obstetricians stage Ib to IVa cervical cancer patients treated with (chemo)radiation between January 1980 and December 2006 were collected. Clinicopathologic and follow-up data were prospectively obtained during standard treatment and follow-up. Protein expression of EGFR, phosphorylated EGFR (pEGFR), PTEN, phosphorylated AKT, and phosphorylated extracellular signal-regulated kinase (pERK) was assessed by immunohistochemistry on tissue microarrays. Results: EGFR staining was present in 35.3%, pEGFR in 19.7%, PTEN in 34.1%, phosphorylated AKT in 4.1%, and pERK in 29.2% of tumors. pEGFR staining was related to PTEN (P = 0.001) and pERK staining (P = 0.004). EGFR staining was inversely related to PTEN (P = 0.011). In multivariate analysis, membranous staining of EGFR [hazard ratio (HR), 1.84; 95% confidence interval (95% CI), 1.20-2.82; P = 0.005] and cytoplasmic staining of pEGFR (HR, 1.71; 95% CI, 1.11-2.66; P = 0.016) were independent predictors of poor response to (chemo)radiation. Membranous EGFR staining also was an independent prognostic factor for poor disease-specific survival (HR, 1.54; 95% CI, 1.09-2.17; P = 0.014). Conclusions: EGFR and pEGFR immunostainings are frequently observed and independently associated with poor response to therapy and disease-specific survival in cervical cancer patients primarily treated by (chemo)radiation. Our data present the EGFR pathway as a promising therapeutic target in already ongoing clinical trials. (Clin Cancer Res 2009;15(23):7389–97)
Breastfeeding, early growth and later obesity

This paper was commissioned by the Foresight programme of the Office of Science and Innovation, Department of Trade and Industry © 2007 Queen’s Printer and Controller of HMSO; published with permission Journal compilation © 2007 The International Association for the Study of Obesity. obesity reviews 8 (Suppl. 1) , 51–54 51 obesity reviews (2007) 8 (Suppl. 1) , 51–54 OnlineOpen: This article is available free online at www.blackwell-synergy.com Blackwell Publishing LtdOxford, UKOBRObesity Reviews1467-7881© 2007 Queen’s Printer and Controller of HMSO; published with permission; Journal compilation © 2007 The International Association for the Study of Obesity ? 20078 ••5154Review Article Breastfeeding, early growth and later obesity A. Singhal & J. Lanigan
Sglt-2 inhibitors for treating metabolic disorders in patients treated with neuroleptic agents

본 발명은 환자에게 SGLT2 억제제를 투여함을 포함하는, 신경이완제로 치료하여 환자에서 유도된 대사 장애를 예방하거나, 상기 대사 장애의 진행을 완화시키거나, 상기 대사 장애를 지연시키거나, 치료하기 위한 방법에 관한 것이다.
Pharmacokinetics and Safety of Green Tea Polyphenols after Multiple-Dose Administration of Epigallocatechin Gallate and Polyphenon E in Healthy Individuals 1

Purpose: Green tea and green tea polyphenols have been shown to possess cancer preventive activities in preclinical model systems. In preparation for future green tea intervention trials, we have conducted a clinical study to determine the safety and pharmacokinetics of green tea polyphenols after 4 weeks of daily p.o. administration of epigallocatechin gallate (EGCG) or Polyphenon E (a defined, decaffeinated green tea polyphenol mixture). In an exploratory fashion, we have also determined the effect of chronic green tea polyphenol administration on UV-induced erythema response. Experimental Design: Healthy participants with Fitzpatric skin type II or III underwent a 2-week run-in period and were randomly assigned to receive one of the five treatments for 4 weeks: 800 mg EGCG once/day, 400 mg EGCG twice/day, 800 mg EGCG as Polyphenon E once/day, 400 mg EGCG as Polyphenon E twice/day, or a placebo once/day (8 subjects/group). Samples were collected and measurements performed before and after the 4-week treatment period for determination of safety, pharmacokinetics, and biological activity of green tea polyphenol treatment. Results: Adverse events reported during the 4-week treatment period include excess gas, upset stomach, nausea, heartburn, stomach ache, abdominal pain, dizziness, headache, and muscle pain. All of the reported events were rated as mild events. For most events, the incidence reported in the polyphenol-treated groups was not more than that reported in the placebo group. No significant changes were observed in blood counts and blood chemistry profiles after repeated administration of green tea polyphenol products. There was a >60% increase in the area under the plasma EGCG concentration-time curve after 4 weeks of green tea polyphenol treatment at a dosing schedule of 800 mg once daily. No significant changes were observed in the pharmacokinetics of EGCG after repeated green tea polyphenol treatment at a regimen of 400 mg twice daily. The pharmacokinetics of the conjugated metabolites of epigallocatechin and epicatechin were not affected by repeated green tea polyphenol treatment. Four weeks of green tea polyphenol treatment at the selected dose and dosing schedule did not provide protection against UV-induced erythema. Conclusions: We conclude that it is safe for healthy individuals to take green tea polyphenol products in amounts equivalent to the EGCG content in 8–16 cups of green tea once a day or in divided doses twice a day for 4 weeks. There is a >60% increase in the systemic availability of free EGCG after chronic green tea polyphenol administration at a high daily bolus dose (800 mg EGCG or Polyphenon E once daily).