Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual A High-Coverage Genome Sequence from an Archaic Denisovan

, 222 (2012); 338 Science et al. Matthias Meyer Individual A High-Coverage Genome Sequence from an Archaic Denisovan This copy is for your personal, non-commercial use only. clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others here. following the guidelines can be obtained by Permission to republish or repurpose articles or portions of articles ): December 3, 2013 www.sciencemag. org (this information is current as of The following resources related to this article are available online at http://www.sciencemag. org/content/338/6104/222.full. html version of this article at: including high-resolution figures, can be found in the online Updated information and services, http://www.sciencemag. org/content/suppl/2012/08/29/science.1224344. DC1.html can be found at: Supporting Online Material http://www.sciencemag. org/content/338/6104/222.full. html#related found at: can be related to this article A list of selected additional articles on the Science Web sites http://www.sciencemag. org/content/338/6104/222.full. html#ref-list-1 , 60 of which can be accessed free: cites 191 articles This article http://www.sciencemag. org/content/338/6104/222.full. html#related-urls 31 articles hosted by HighWire Press; see: cited by This article has been http://www.sciencemag. org/cgi/collection/genetics Genetics subject collections: This article appears in the following
Evaluation of an evidence-based intervention implemented with African-American women to prevent substance abuse, strengthen relationship skills and reduce risk for HIV/AIDS

ABSTRACT African-American females in the U.S. are disproportionately affected by HIV/AIDS, and a large majority of new infections in this population are attributed to heterosexual contact. Risk factors include substance abuse, lack of knowledge about male partners’ possible HIV infection risk, incarceration, disruptions of social networks, and intimate partner violence. This study assessed the effects of a comprehensive, evidence-based prevention intervention, Creating Lasting Family Connections (CLFC) that was implemented with sensitivity to African-American females, using a quasi-experimental design. The CLFC program was implemented with 175 women and their results were compared to a convenience sample of 44 women who were similar on background characteristics. Results showed significant (p < .05, two-tailed) increases in the proportion of individuals getting HIV tested and getting the results from these tests, a larger decrease in intimate partner abuse within the past three months, and larger increases in three relationship skills (emotional expression, interpersonal skills, and relationship satisfaction) relative to the comparison group.
Identification of Volatiles Produced by Cladosporium cladosporioides CL-1, a Fungal Biocontrol Agent That Promotes Plant Growth

Certain microbial Volatile Organic Compounds (VOCs) have been reported to enhance the growth and development of plants. The biocontrol fungi, Cladosporium cladosporioides CL-1 significantly improved the growth of tobacco seedlings in vitro when they were co-cultivated without physical contact. SPME Quadrupole GC/MS/MS revealed that CL-1 emited the volatiles α-pinene, (−)-trans-caryophyllene, tetrahydro-2,2,5,5-tetramethylfuran, dehydroaromadendrene, and (+)-sativene. Potential roles of these volatiles in plant growth and development are discussed. Even though there were several fungal VOCs reported in the past that could influence plant growth, their exact mechanisms of action are not fully known. Fungal VOC-mediated plant growth promotion requires in-depth study in order for this technology to be used in large scale for crops, especially those grown under greenhouse conditions.
Psychic trauma. Return of images after a stress film.

SOME PERSONS who experience psychic trauma report that memories of the precipitating event intrusively enter their awareness long after the traumatic event takes place. Such clinical observations have led to the theory that there is a compulsion to re-enact traumas, perhaps as a belated attempt at mastery. This paper reports an experimental study of this theory in which a stressful film induced subsequent unbidden images in volunteer subjects. The Repetition of Psychic Trauma. —Freud and Breuer1described psychic trauma as an event in which perceptual and affective stimuli overwhelm the processes that ordinarily bind them and maintain homeostasis. These stimuli tend to return to mind, sometimes as visual images. In the "Project for a Scientific Psychology,''2Freud calls such vivid images ``untamed memories. " When affects associated with the trauma are worked through, the memories become "tamed"; that is, reduced in intensity and sensory quality. But, if conflict interferes
A study of bright Southern long period variables

In this paper we present radial velocity curves of AGB variables that exhibit various kinds of anomalies: semiregular variables (SRVs) with typical mira periods, SRVs exceeding the mira 2.5 mag amplitude limit, miras with secondary maxima in their light curves, and a SRV with a long secondary period. The stars with reliable Hipparcos parallaxes from this and from previous studies are plotted in a log P-M K -diagram. Our objects nicely follow the log P-M K -relations determined for the LMC. This allows the pulsation mode to be identified. While all miras fall on the fundamental mode sequence, the SRVs fall on both the first overtone and fundamental mode sequences. The SRVs on the fundamental mode sequence occur at both high and low luminosities, some of them being more luminous than larger amplitude miras. This demonstrates observationally that some parameter other than luminosity affects the stability of long period variables, probably mass. First overtone pulsators all show velocity amplitudes around 4 km s -1 . For the fundamental mode pulsators, the velocity amplitude shows a correlation with light amplitude. The two miras R Cen and R Nor, known for their double-peaked light curves, have velocity curves that are quite different. The R Nor velocity curve shows no evidence of the double peaks, meaning that the true pulsation period is the time between alternate minima or maxima. There is slight evidence for a double bump in the R Cen velocity curve. It is suggested that these stars are relatively massive (3-5 M ○. ).
Möbius Syndrome: Evidence for a Vascular Etiology

We report five infants with restricted lateral gaze, facial diplegia, feeding difficulty, and/or respiratory disorders without significant pulmonary disease. Viral studies were negative in all patients. Two children had radiologic findings that included brain-stem hypoplasia and symmetric calcification in the dorsal tectum at the junction of the midbrain and pons. Autopsy of one of these two children demonstrated capillary telangiectasia in the mesencephalon and pons. The other three children had normal computed tomographic (CT) scans. However, their autopsies revealed focal brain-stem necrosis with calcifications but without vascular malformation. We suggest that the capillary malformations in one of our patients directly resulted in a vascular-induced necrosis and the manifestation of Möbius sequence. The similarity of symmetric neuropathologic findings in the three other patients and the CT scan in the one surviving patient suggest focal hemodynamic changes restricted to the posterior circulation, indirectly supporting a vascular theory of embryopathogenesis. (J Child Neurol 1993;8:260-265).
ECT in Texas: 19 months of mandatory reporting.

BACKGROUND Texas law requires that all non-federal clinical facilities providing electroconvulsive therapy (ECT) report every treatment to the state's mental health agency. The resulting data provide total population information about treating physicians and hospitals; payment source; patient age, sex, ethnicity, diagnosis, and admission/consent status; symptom severity and response; numbers and types of treatments; and untoward events occurring within 14 days after treatment. METHOD We reviewed all reports of ECT between September 1993 and April 1995 (2583 reports, approximately 15,240 treatments). RESULTS About 6% (N = 117) of Texas psychiatrists performed ECT during the period, at 50 hospitals. One of 13 state-funded mental institutions performed ECT on-site; some occasionally contracted with private hospitals. Almost all patients (88.1%) were white. Some older age groups received proportionately more ECT than younger groups, but no sharp increase was associated with eligibility for Medicare. Five patients were less than 18 years of age; 70.3% were female. Virtually all patients (99.0%) consented to the treatment themselves (rather than by guardian), including committed-but-consenting patients (1.5%). Reports (5.8%) described multiple-monitored treatment (MMECT, not depatterning). Group data indicated generally good-to-excellent response, as measured by a five-point symptom-severity scale. Eight patients died within 14 days of a treatment, 2 possibly of anesthesia complications and 3 others in accidents or by suicide. Four were receiving maintenance treatments (generally about every other week). No death appeared related to ECT stimulus or seizure. CONCLUSION ECT in Texas is performed by a small minority of psychiatrists and is unavailable to many patients who need it. It is most accessible to white patients who receive care outside the public sector. Our data support the common finding that ECT is generally safe and effective.
Type of manuscript: Original Article Manuscript title: Exposure to second hand smoke and reproductive outcomes depending on maternal asthma

Affiliations: 1. Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain 2. Municipal Institute of Medical Research, Barcelona, Spain 3. Universitat Pompeu Fabra, Barcelona, Spain 4. CIBER Epidemiologia y Salud Pública (CIBERESP), Spain 5. Departamento de Sanidad Gobierno Vasco, Laboratorio Normativo de Salud Pública, Spain 6. University of Basque Country, EHU-UPV, Spain 7. Public Health Research Institute, Valencia, Spain 8. Universidad de Oviedo, Spain 9. Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece. 10. School of Public Health, Athens, Greece
Global Transcriptome Analysis of Genetically Identified Neurons in the Adult Cortex

The enormous cellular complexity of the brain is a major obstacle for gene expression profiling of neurological disease models, because physiologically relevant changes of transcription in a specific neuronal subset are likely to be lost in the presence of other neurons and glia. We solved this problem in transgenic mice by labeling genetically defined cells with a nuclear variant of GFP. When combined with laser-directed microdissection, intact RNA from unfixed, freeze-dried sections can be isolated, which is a prerequisite for high-quality global transcriptome analysis. Here, we compared gene expression profiles between pyramidal motor neurons and pyramidal somatosensory neurons captured from layer V of the adult neocortex. One striking feature of motor neurons is the elevated expression of ribosomal genes and genes involved in ATP synthesis. This suggests a molecular adaptation of the upper motor neurons to longer axonal projections and higher electrical activity. These molecular signatures were not detected when cortical layers and microareas were analyzed in toto. Additionally, we used microarrays to determine the global mRNA expression profiles of microdissected Purkinje cells and cellularly complex cerebellar cortex microregions. In summary, our analysis shows that cellularly complex targets lead to averaged gene expression profiles that lack substantial amounts of cell type-specific information. Thus, cell type-restricted sampling strategies are mandatory in the CNS. The combined use of a genetic label with laser-microdissection offers an unbiased approach to map patterns of gene expression onto practically any cell type of the brain.
Duration of Diabetes Mellitus and Risk of Thromboembolism and Bleeding in Atrial Fibrillation: Nationwide Cohort Study

Background and Purpose— Guidelines advocate anticoagulant treatment to all patients with atrial fibrillation and concomitant diabetes mellitus. The potential refinement to thromboembolic risk stratification that may spring from subdividing diabetes mellitus is unexplored. The purpose was to investigate duration of diabetes mellitus as a predictor of thromboembolism and anticoagulant-related bleeding in patients with atrial fibrillation. Methods— Using nationwide Danish registries, we identified all patients discharged from hospital with an incident diagnosis of atrial fibrillation from 2000 to 2011. Hazard ratios with 95% confidence intervals for thromboembolism and bleeding according to years of diabetes mellitus duration in categories (0–4, 5–9, 10–14, and ≥15) and as a continuous variable using cubic splines were calculated by Cox regression. Results— The study population comprised 137 222 patients with atrial fibrillation, of which 12.4% had diabetes mellitus. Compared with patients without diabetes mellitus and after adjustment for anticoagulant treatment and CHA2DS2-VASc components (congestive heart failure, hypertension, age, previous stroke, vascular disease, and sex), the risk of thromboembolism was lowest in the 0 to 4 years duration category (hazard ratio, 1.11; 95% confidence interval, 1.03–1.20), and highest in the longest duration category of ≥15 years (hazard ratio, 1.48; 95% confidence interval, 1.29–1.70). When analyzed as a continuous variable, duration of diabetes mellitus was associated with risk of thromboembolism in a dose-response-dependent manner, but not with a higher risk of bleeding during anticoagulant treatment. Conclusions— In patients with atrial fibrillation, longer duration of diabetes mellitus was associated with a higher risk of thromboembolism, but not with a higher risk of anticoagulant-related bleeding. Considering the critical balance between preventing thromboembolism and avoiding bleeding, longer duration of diabetes mellitus may favor initiation of anticoagulant therapy.
PKC Theta Ablation Improves Healing in a Mouse Model of Muscular Dystrophy

Inflammation is a key pathological characteristic of dystrophic muscle lesion formation, limiting muscle regeneration and resulting in fibrotic and fatty tissue replacement of muscle, which exacerbates the wasting process in dystrophic muscles. Limiting immune response is thus one of the therapeutic options to improve healing, as well as to improve the efficacy of gene- or cell-mediated strategies to restore dystrophin expression. Protein kinase C θ (PKCθ) is a member of the PKCs family highly expressed in both immune cells and skeletal muscle; given its crucial role in adaptive, but also innate, immunity, it is being proposed as a valuable pharmacological target for immune disorders. In our study we asked whether targeting PKCθ could represent a valuable approach to efficiently prevent inflammatory response and disease progression in a mouse model of muscular dystrophy. We generated the bi-genetic mouse model mdx/θ−/−, where PKCθ expression is lacking in mdx mice, the mouse model of Duchenne muscular dystrophy. We found that muscle wasting in mdx/θ−/− mice was greatly prevented, while muscle regeneration, maintenance and performance was significantly improved, as compared to mdx mice. This phenotype was associated to reduction in inflammatory infiltrate, pro-inflammatory gene expression and pro-fibrotic markers activity, as compared to mdx mice. Moreover, BM transplantation experiments demonstrated that the phenotype observed was primarily dependent on lack of PKCθ expression in hematopoietic cells. These results demonstrate a hitherto unrecognized role of immune-cell intrinsic PKCθ activity in the development of DMD. Although the immune cell population(s) involved remain unidentified, our findings reveal that PKCθ can be proposed as a new pharmacological target to counteract the disease, as well as to improve the efficacy of gene- or cell- therapy approaches.
Human TLR10 Is a Functional Receptor, Expressed by B Cells and Plasmacytoid Dendritic Cells, Which Activates Gene Transcription through MyD881

Human TLR10 is an orphan member of the TLR family. Genomic studies indicate that TLR10 is in a locus that also contains TLR1 and TLR6, two receptors known to function as coreceptors for TLR2. We have shown that TLR10 was not only able to homodimerize but also heterodimerized with TLRs 1 and 2. In addition, unlike TLR1 and TLR6, TLR10 was expressed in a highly restricted fashion as a highly N-glycosylated protein, which we detected in B cell lines, B cells from peripheral blood, and plasmacytoid dendritic cells from tonsil. We were also able to detect TLR10 in a CD1a+ DC subset derived from CD34+ progenitor cells which resemble Langerhans cells in the epidermis. Although we were unable to identify a specific ligand for TLR10, by using a recombinant CD4TLR10 molecule we also demonstrated that TLR10 directly associates with MyD88, the common Toll IL-1 receptor domain adapter. Additionally, we have characterized regions in the Toll IL-1 receptor domain of TLR10 that are essential in the activation of promoters from certain inflammatory cytokines. Even though TLR10 expression has not been detected in mice, we have identified a partial genomic sequence of the TLR10 gene that was present but nonfunctional and disrupted by a retroviral insertion in all mouse strains tested. However, a complete TLR10 sequence could be detected in the rat genome, indicating that a functional copy may be preserved in this species.
Effect of acidosis on Ca 2 1 uptake and release by sarcoplasmic reticulum of intact rat ventricular myocytes

Hulme, J. T. , and C. H. Orchard. Effect of acidosis on Ca21 uptake and release by sarcoplasmic reticulum of intact rat ventricular myocytes. Am. J. Physiol. 275 (Heart Circ. Physiol. 44): H977–H987, 1998. —The effect of acidosis on Ca21 uptake and release by the sarcoplasmic reticulum (SR) of rat ventricular myocytes has been investigated. Intracellular Ca21 concentration ([Ca]i) was monitored using fura 2; the L-type Ca21 current (ICa) was monitored using the perforated patch-clamp technique. Acidosis was produced either by superfusing the cells with an acid solution (intracellular and extracellular acidosis) or by NH4Cl withdrawal (intracellular acidosis). Both types of acidosis increased the amplitude, and slowed the declining phase, of the Ca21 transient. Application of caffeine produced a rise of [Ca]i, which declined in the continued presence of caffeine; the declining phase was slowed by the acid solution but was unaffected by NH4Cl withdrawal. Acidosis decreased the fraction of the caffeineinduced release that was released by electrical stimulation but had no effect on ICa. It is concluded that acidosis inhibits SR Ca21 uptake and Ca21-induced Ca21 release in intact myocytes but that these effects are compensated by an increase in SR Ca21 content secondary to a rise in cytoplasmic [Ca21].
Down-Regulation of PERK-ATF4-CHOP Pathway by Astragaloside IV is Associated with the Inhibition of Endoplasmic Reticulum Stress-Induced Podocyte Apoptosis in Diabetic Rats

Background: Endoplasmic reticulum (ER) stress-induced podocyte apoptosis plays a critical role in the development of diabetic nephropathy (DN). Here, we tested the hypothesis that suppression of PERK-ATF4-CHOP pathway by Astragaloside IV (AS-IV) is associated with inhibition of ER stress-induced podocyte apoptosis in streptozotocin (STZ)-induced diabetic rats. Methods: Diabetic rats were treated with AS-IV at 5 and 10 mg· kg-1· d-1, p.o. , for 12 weeks. Albuminuria examination, hematoxylin & eosin staining and TUNEL analysis were performed. Immunohistochemistry, western blot, and real-time PCR were used to detect renal expression of ER chaperone GRP78 and ER-associated apoptosis proteins. Results: Treatment with AS-IV ameliorated albuminuria and renal histopathology in diabetic rats. Diabetic rats had significant increment in podocyte apoptosis as well as phosphorylated PERK and eIF2α in the kidneys, which were attenuated by AS-IV treatment. Furthermore, diabetic rats were found to have increased protein and mRNA expressions of GRP78 and ER-associated apoptosis proteins, such as ATF4, CHOP and TRB3, which were also attenuated by AS-IV treatment. Increased Bax expression and decreased Bcl-2 expression were detected in diabetic rats, and these changes were partially restored by AS-IV treatment. Conclusion: The protective effect of AS-IV on ER stress-induced podocyte apoptosis is associated with inhibition of PERK-ATF4-CHOP pathway. Down-regulation of PERK- ATF4-CHOP pathway by AS-IV may be a novel strategy for the treatment of DN.
Comparison of CCL28, interleukin-8, interleukin-1β and tumor necrosis factor-alpha in subjects with gingivitis, chronic periodontitis and generalized aggressive periodontitis.

BACKGROUND AND OBJECTIVE Cytokines produced by various cells are strong local mediators of inflammation. Mucosa-associated epithelial chemokine (CCL28), interleukin-8 (IL-8), interleukin-1beta (IL-1β) and tumor necrosis factor-alpha (TNF-α) are major cytokines that play important roles in the periodontal inflammatory process. In this study we aimed to compare the levels of CCL28, IL-8, IL-1β and TNF-α in the gingival crevicular fluid of both periodontally healthy subjects and in subjects diagnosed with gingivitis, chronic periodontitis and generalized aggressive periodontitis. MATERIAL AND METHODS A total of 84 subjects participated in the study: 21 subjects had gingivitis, 21 subjects had chronic periodontitis, 21 subjects had generalized aggressive periodontitis and 21 were periodontally healthy. The levels of CCL28, IL-8, IL-1β and TNF-α were analyzed using enzyme-linked immune sorbent assay (ELISA). RESULTS The total levels of CCL28 and IL-8 in the gingival crevicular fluid of the generalized aggressive periodontitis group (324.74 ± 42.62 pg/30 s, 487.62 ± 49.21 pg/30 s) were significantly higher than those of the chronic periodontitis group (268.81 ± 28.64 pg/30 s, 423.65 ± 35.24 pg/30 s), the gingivitis group (146.35 ± 17.46 pg/30 s, 310.24 ± 48.20 pg/30 s) and the periodontally healthy group (92.46 ± 22.04 pg/30 s, 148.41 ± 24.64 pg/30 s). Similarly, the total levels of IL-1β and TNF-α in the generalized aggressive periodontitis group (110.23 ± 9.20 pg/30 s, 1284.46 ± 86.32 pg/30 s) were significantly higher than those in the chronic periodontitis group (423.65 ± 35.24 pg/30 s, 82.64 ± 9.12 pg/30 s), the gingivitis group (52.10 ± 7.15 pg/30 s, 824.24 ± 44.68 pg/30 s) and the periodontally healthy group (36.44 ± 8.86 pg/30 s, 628.26 ± 34.61 pg/30 s). CONCLUSION CCL28, IL-8, IL-1β and TNF-α may play key roles in the host response to inflammation in periodontal diseases. As the severity of periodontal diseases increases, destruction of periodontal tissues also increases. Inflammation is one among many factors that trigger periodontal tissue destruction. Identification of the mediators that influence the development and progression of inflammation in periodontal diseases may be very important in understanding the prognoses of periodontal diseases.