Miracle-dz/UniFAR-FTUs huggingface dataset:
Controlling false discoveries in genome scans for selection

Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Based on statistical models, these genomewide testing procedures have attracted considerable attention as tools to identify loci potentially targeted by natural selection. An important issue with PD and EA tests is that incorrect model specification can generate large numbers of false‐positive associations. Spurious association may indeed arise when shared demographic history, patterns of isolation by distance, cryptic relatedness or genetic background are ignored. Recent works on PD and EA tests have widely focused on improvements of test corrections for those confounding effects. Despite significant algorithmic improvements, there is still a number of open questions on how to check that false discoveries are under control and implement test corrections, or how to combine statistical tests from multiple genome scan methods. This tutorial study provides a detailed answer to these questions. It clarifies the relationships between traditional methods based on allele frequency differentiation and EA methods and provides a unified framework for their underlying statistical tests. We demonstrate how techniques developed in the area of genomewide association studies, such as inflation factors and linear mixed models, benefit genome scan methods and provide guidelines for good practice while conducting statistical tests in landscape and population genomic applications. Finally, we highlight how the combination of several well‐calibrated statistical tests can increase the power to reject neutrality, improving our ability to infer patterns of local adaptation in large population genomic data sets.
Mortality and Morbidity Due to Exposure to Ambient NO2, SO2, and O3 in Isfahan in 2013–2014

Background: The presence of air pollutants such as CO, NO2, SO2, O3, and PM in the ambient air mainly emitted from fossil fuels combustion has become a major health concern. The aims of this study were to estimate the attribution of NO2, SO2, and O3 in the premature deaths and prevalence of cardiovascular and respiratory diseases in Isfahan in 2013–2014. Methods: In this study, short-term health effects (total mortality, cardiovascular and respiratory mortality, chronic obstructive pulmonary disease, and acute myocardial infarction) of exposure NO2, SO2, and O3 on the population of Isfahan were assessed using AirQ 2.2. 3 software suggested by the World Health Organization (WHO). Results: The result showed that from nonaccident total mortality in 2013–2014 in Isfahan, the attributable proportion related to NO2, SO2, and O3 were 1.03% (109 cases), 3.46% (365 cases), and 1.29% (136 cases), respectively. The percentage of days that people were exposed to the highest concentration of NO2 (40–49 μg/m3), SO2 (60–69 μg/m3), and O3 (40–49 μg/m3) was 34.46%, 16.85%, and 42.74% of a year, respectively. Total mortality attributed to NO2, SO2, and O3 exposure was 0.36%, 0.79%, and 0.83%, respectively. Conclusions: The concentrations of NO2 and SO2 were upper than the WHO guidelines. The Air-Q software in spite of its limitations can provide useful information regarding the health outcome of the air pollutants. The results estimated in this study were considerable. This information can help the health authorities and policy makers to draw suitable strategies and fulfill effective emission control programs.
Trophic effects of adipose-tissue-derived and bone-marrow-derived mesenchymal stem cells enhance cartilage generation by chondrocytes in co-culture

Aims Combining mesenchymal stem cells (MSCs) and chondrocytes has great potential for cell-based cartilage repair. However, there is much debate regarding the mechanisms behind this concept. We aimed to clarify the mechanisms that lead to chondrogenesis (chondrocyte driven MSC-differentiation versus MSC driven chondroinduction) and whether their effect was dependent on MSC-origin. Therefore, chondrogenesis of human adipose-tissue-derived MSCs (hAMSCs) and bone-marrow-derived MSCs (hBMSCs) combined with bovine articular chondrocytes (bACs) was compared. Methods hAMSCs or hBMSCs were combined with bACs in alginate and cultured in vitro or implanted subcutaneously in mice. Cartilage formation was evaluated with biochemical, histological and biomechanical analyses. To further investigate the interactions between bACs and hMSCs, (1) co-culture, (2) pellet, (3) Transwell® and (4) conditioned media studies were conducted. Results The presence of hMSCs–either hAMSCs or hBMSCs—increased chondrogenesis in culture; deposition of GAG was most evidently enhanced in hBMSC/bACs. This effect was similar when hMSCs and bAC were combined in pellet culture, in alginate culture or when conditioned media of hMSCs were used on bAC. Species-specific gene-expression analyses demonstrated that aggrecan was expressed by bACs only, indicating a predominantly trophic role for hMSCs. Collagen-10-gene expression of bACs was not affected by hBMSCs, but slightly enhanced by hAMSCs. After in-vivo implantation, hAMSC/bACs and hBMSC/bACs had similar cartilage matrix production, both appeared stable and did not calcify. Conclusions This study demonstrates that replacing 80% of bACs by either hAMSCs or hBMSCs does not influence cartilage matrix production or stability. The remaining chondrocytes produce more matrix due to trophic factors produced by hMSCs.
Effects of partial substitution of ni by pd on thermoelectric properties of ZrNiSn-based compounds

The ZrNiSn-based half-Heusler compounds crystallize in a cubic structure of the MgAgAs type, and belong to semiconductors with narrow band gaps. Due to promising potential as new thermoelectric materials, they have attracted much attention in recent years. In the present paper, compounds with Pd partial substitution on the Ni sites, were successfully synthesized by solid state reaction method. Effects of such substitution on the thermoelectric properties were mainly studied. It is shown that, the substitution of Pd for Ni resulted in a significant reduction in the thermal conductivity. The Seebeck coefficient also decreased, but only by a small amount. In a Hf/sub 0.5/Zr/sub 0.5/Ni/sub 0.8/Pd/sub 0.2/Sn/sub 0.99/Sb/sub 0.01/ compound, a power factor of 19.5 /spl mu/W/cm-K/sup 2/ and a thermal conductivity as low as of 4.5 W/m-K were measured at room temperature. The dimensionless figure of merit, ZT, increased with increasing temperature and reached a maximum value of 0.7 at about 800 K.
The Europeanization of Health Care Governance - Implementing the Market Imperatives of Europe

The paper examines the Europeanization process and the impact of the European Union (EU) on national healthcare policies, using the example of Denmark. The analysis reveals that although health policy formally falls within the competence of member states, the impact of the EU is becoming increasingly conspicuous and has contributed to a gradual restructuring of healthcare boundaries as well as of some of its organizing principles. Furthermore, the process and impact have a de-structuring effect on the more traditional governance tools used in relation to healthcare. The paper concludes that the EU has a signifi cant impact and that we may be witnessing the formation of a new institutional legacy that represents the initiation of a Europeanized healthcare model: a model emerging around a new set of stakeholders, principles and structures, which includes the market, principles of free movement, patient choice and patient rights institutionalized and safeguarded by the EU.
Nectin-like 4 Complexes with Choline Transporter-like Protein-1 and Regulates Schwann Cell Choline Homeostasis and Lipid Biogenesis in Vitro*

Nectin-like 4 (NECL4, CADM4) is a Schwann cell-specific cell adhesion molecule that promotes axo-glial interactions. In vitro and in vivo studies have shown that NECL4 is necessary for proper peripheral nerve myelination. However, the molecular mechanisms that are regulated by NECL4 and affect peripheral myelination currently remain unclear. We used an in vitro approach to begin identifying some of the mechanisms that could explain NECL4 function. Using mass spectrometry and Western blotting techniques, we have identified choline transporter-like 1 (CTL1) as a putative complexing partner with NECL4. We show that intracellular choline levels are significantly elevated in NECL4-deficient Schwann cells. The analysis of extracellular d9-choline uptake revealed a deficit in the amount of d9-choline found inside NECL4-deficient Schwann cells, suggestive of either reduced transport capabilities or increased metabolization of transported choline. An extensive lipidomic screen of choline derivatives showed that total phosphatidylcholine and phosphatidylinositol (but not diacylglycerol or sphingomyelin) are significantly elevated in NECL4-deficient Schwann cells, particularly specific subspecies of phosphatidylcholine carrying very long polyunsaturated fatty acid chains. Finally, CTL1-deficient Schwann cells are significantly impaired in their ability to myelinate neurites in vitro. To our knowledge, this is the first demonstration of a bona fide cell adhesion molecule, NECL4, regulating choline homeostasis and lipid biogenesis. Phosphatidylcholines are major myelin phospholipids, and several phosphorylated phosphatidylinositol species are known to regulate key aspects of peripheral myelination. Furthermore, the biophysical properties imparted to plasma membranes are regulated by fatty acid chain profiles. Therefore, it will be important to translate these in vitro observations to in vivo studies of NECL4 and CTL1-deficient mice.
Validity of the K-10 in detecting DSM-IV-defined depression and anxiety disorders among HIV-infected individuals

Abstract It has been suggested that an HIV diagnosis may increase the likelihood of mental disorders among infected individuals and that the progression of HIV may be hastened by mental disorders like anxiety and depression. Therefore, a brief screening measure, with good sensitivity/specificity for psychiatric diagnoses that could be given to HIV-infected individuals would be useful. We assessed the validity of the K-10, using the MINI International Neuropsychiatric Interview as the gold standard, in a sample of 429 HIV-infected adults enrolled in HIV care and treatment services near Cape Town, South Africa. There was significant agreement between the K-10 and the MINI-defined depressive and anxiety disorders. A receiver operating characteristic (ROC) curve analysis indicated that the K-10 showed agreeable sensitivity and specificity in detecting depression (area under the ROC curve, 0.77), generalized anxiety disorder (0.78), and posttraumatic stress disorder (PTSD) (0.77). The K-10 may be a useful screening measure for detecting mood and anxiety disorders, including PTSD, in patients with HIV/AIDS.
Patterns of Signs That Telephone Crisis Support Workers Associate with Suicide Risk in Telephone Crisis Line Callers

Signs of suicide are commonly used in suicide intervention training to assist the identification of those at imminent risk for suicide. Signs of suicide may be particularly important to telephone crisis-line workers (TCWs), who have little background information to identify the presence of suicidality if the caller is unable or unwilling to express suicidal intent. Although signs of suicide are argued to be only meaningful as a pattern, there is a paucity of research that has examined whether TCWs use patterns of signs to decide whether a caller might be suicidal, and whether these are influenced by caller characteristics such as gender. The current study explored both possibilities. Data were collected using an online self-report survey in a Australian sample of 137 TCWs. Exploratory factor analysis uncovered three patterns of suicide signs that TCWs may use to identify if a caller might be at risk for suicide (mood, hopelessness, and anger), which were qualitatively different for male and female callers. These findings suggest that TCWs may recognise specific patterns of signs to identify suicide risk, which appear to be influenced to some extent by the callers’ inferred gender. Implications for the training of telephone crisis workers and others including mental-health and medical professionals, as well as and future research in suicide prevention are discussed.
Fire resistance and reaction-to-fire of Shorea macrophylla and Acacia mangium particleboards treated with boron and phosphorous-based fire retardants

Fire resistance and reaction-to-fire of Engkabang ( Shorea macrophylla) and Acacia mangium particleboards, which were treated with zinc borate (ZBr) and monoammonium phosphate (MAP), were investigated in this study. Ten percent of the fire retardants were incorporated into the particleboards in powder form during resin-particle mixing process. The fire resistance of the boards was assessed using insulation and integrity failures. Meanwhile, reaction-to-fire was conducted to examine the effectiveness of the fire retardants to delay ignition and reduce weight loss. The study showed that ZBr was excellent in improving insulation and integrity failures of the boards as compared to MAP. Zinc borate delayed the increase of unexposed face temperature up to 18 min and reduced the weight loss down to 0.57% (ZBr-treated A. mangium), but MAP was shown to be better than ZBr in delaying ignition (i.e. up to 41s for A. mangium and 20s for S. macrophylla). The ineffectiveness of the fire retardants to reduce weight loss of the boards (MAP-treated and ZBr-treated S. macrophylla and MAP-treated A. mangium might be due to leaching and volatization of phosphoric acid and boric acid in the formulations of the particleboards which would then cause the chemical loading to be lower than the actual chemical loading. It is suggested to extend the research especially in determining the chemical loading of each treated boards during and after they are exposed to fire. This is essential to prove the claim that chemical loading is decreased due to the leaching of phosphoric acid and volatization of boric acid.
Event-Related Potential Measures of Attention Capture in Adolescent Inpatients With Acute Suicidal Behavior

Impaired executive functions, modulated by the frontal lobes, have been suggested to be associated with suicidal behavior. The present study examines one of these executive functions, attentional control, maintaining attention to the task-at-hand. A group of inpatient adolescents with acute suicidal behavior and healthy controls were studied using a passively presented auditory optimal paradigm. This “optimal” paradigm consisted of a series of frequently presented homogenous pure tone “standards” and different “deviants,” constructed by changing one or more features of the standard. The optimal paradigm has been shown to be a more time-efficient replacement to the traditional oddball paradigm, which makes it suitable for use in clinical populations. The extent of processing of these “to-be-ignored” auditory stimuli was measured by recording event-related potentials (ERPs). The P3a ERP component is thought to reflect processes associated with the capturing of attention. Rare and novel stimuli may result in an executive decision to switch attention away from the current cognitive task and toward a probe of the potentially more relevant “interrupting” auditory input. On the other hand, stimuli that are quite similar to the standard should not elicit P3a. The P3a has been shown to be larger in immature brains in early compared to later adolescence. An overall enhanced P3a was observed in the suicidal group. The P3a was larger in this group for both the environmental sound and white noise deviants, although only the environmental sound P3a attained significance. Other deviants representing only a small change from the standard did not elicit a P3a in healthy controls. They did elicit a small P3a in the suicidal group. These findings suggest a lowered threshold for the triggering of the involuntary switch of attention in these patients, which may play a role in their reported distractibility. The enhanced P3a is also suggestive of an immature frontal central executive and may provide a promising marker for early identification of some of the risk factors for some of the cognitive difficulties linked to suicidality.
THE CHEMISTRY OF VIBRATIONALLY EXCITED H2 IN THE INTERSTELLAR MEDIUM

The internal energy available in vibrationally excited H2 molecules can be used to overcome or diminish the activation barrier of various chemical reactions of interest for molecular astrophysics. In this paper, we investigate in detail the impact on the chemical composition of interstellar clouds of the reactions of vibrationally excited H2 with C+, He+, O, OH, and CN, based on the available chemical kinetics data. It is found that the reaction of H2 (v>0) and C+ has a profound impact on the abundances of some molecules, especially CH+, which is a direct product and is readily formed in astronomical regions with fractional abundances of vibrationally excited H2, relative to the ground state H2, in excess of ∼10−6, independently of whether the gas is hot or not. The effects of these reactions on the chemical composition of the diffuse clouds ζOph and HD 34078, the dense photon-dominated region (PDR) Orion Bar, the planetary nebula NGC 7027, and the circumstellar disk around the B9 star HD 176386 are investigated through PDR models. We find that formation of CH+ is especially favored in dense and highly FUV illuminated regions such as the Orion Bar and the planetary nebula NGC 7027, where column densities in excess of 1013 cm−2 are predicted. In diffuse clouds, however, this mechanism is found to be not efficient enough to form CH+ with a column density close to the values derived from astronomical observations.
Habitat connectivity improves reserve performance

Connectivity is now a common consideration in conservation planning, but we need further empirical evidence for the role of connectivity in catalyzing reserve function. We examined whether connectivity improved reserve performance by investigating how isolation between coral reefs and mangroves influenced fish assemblages inside and outside a reserve in Moreton Bay, Australia. Connectivity greatly enhanced reserve performance, with close reserve habitats supporting more harvested fish, and a greater abundance of both piscivores and herbivores than similar nonreserve locations. Close reserve habitats also contained fewer prey fish than nonreserve locations. In contrast, fish abundance in isolated reserve habitats did not differ from similar nonreserve locations. We demonstrate that connectivity can improve the performance of a reserve in promoting fish abundance. We highlight its importance for maintaining ecological processes in reserves and advocate the prioritization of areas of similarly connected habitat for conservation.
When Do People Believe That Alcohol Treatment Is Effective ? The Importance of Perceived Client and Therapist Motivation

Respondents read a narrative depicting a drunk-driving offender seeking help for alcohol problems and were randomly assigned to receive 1 of 3 types of client motivation (autonomous motivation, compulsory treatment, or impression management) and 1 of 2 types of therapist motivation (autonomous vs. controlled motivation). Maximal treatment efficacy was expected when both client and therapist were autonomously motivated. Minimal treatment efficacy was expected when the client entered treatment only to manage impressions and when the therapist exhibited controlled motivation. Compulsory treatment undermined beliefs about client interest in treatment. Finally, autonomously motivated therapists were expected to be able to reverse expected negative outcomes for compulsory treatment and impression management clients. It was found that expectations about the efficacy of alcohol aeam~nt were affected by the perceived motivation of clients and therapists.
The Impact of Vitamin D, Calcium, Protein Supplementation, and Physical Exercise on Bone Metabolism After Bariatric Surgery: The BABS Study

Laparoscopic Roux‐en‐Y gastric bypass (RYGB) and sleeve gastrectomy (SG) are common and effective methods to treat severe obesity, but these procedures can adversely influence bone metabolism and areal bone mineral density (aBMD). This was a prospective 24‐month single‐center interventional two‐arm study in 220 women and similarly aged men (median age 40.7 years) with a body mass index (BMI) >38 kg/m2 after RYGB and SG procedures. Patients were randomized into: 1) an intervention group receiving: 28,000 IU cholecalciferol/wk for 8 weeks before bariatric surgery, 16,000 IU/wk and 1000 mg calciummonocitrate/d after surgery, daily BMI‐adjusted protein supplementation and physical exercise (Nordic walking, strength perseverance, and equipment training); 2) a non‐intervention group: no preoperative loading, nutritional supplementation, or obligatory physical exercise. At study endpoint, when comparing the intervention group to the non‐intervention group, the relative percentage changes of serum levels of sclerostin (12.1% versus 63.8%), cross‐linked C‐telopeptide (CTX, 82.6% versus 158.3%), 25‐OH vitamin D (13.4% versus 18.2%), phosphate (23.7% versus 32%, p < 0.001 for all), procollagen type 1 amino‐terminal propeptide (P1NP, 12% versus 41.2%), intact parathyroid hormone (iPTH, –17.3% versus –7.6%), and Dickkopf‐1 (–3.9% versus –8.9%, p < 0.05 for all) differed. The decline in lumbar spine, total hip and total body aBMD, changes in BMI, lean body mass (LBM), as well as changes in trabecular bone score (TBS) values (p < 0.005 for all) were less, but significantly, pronounced in the intervention group. We conclude that vitamin D loading and ongoing vitamin D, calcium, and BMI‐adjusted protein supplementation in combination with physical exercise decelerates the loss of aBMD and LBM after bariatric surgery. Moreover, the well‐known increases of bone turnover markers are less pronounced. © 2015 American Society for Bone and Mineral Research.
CHANGES IN MODELS OF AQUATIC ECOSYSTEMS APPROACHING CARRYING CAPACITY

Using a top-down modeling approach, published mass-balance models of trophic interactions and state variables in the western central Pacific Ocean and the northern Gulf of Mexico shelf were used to explore how large increases in top predator biomasses can be accommodated with given primary productions. It appears that the biomasses of top predators in these models can be increased an order of magnitude, which leads to a six- to sevenfold increase in overall consumer biomasses. This results in changes in food web structures that are in agreement with major aspects of E. P. Odum's theory of ecosystem development, particularly with regard to features associated with the retention and recycling of detritus. Based on the simulations and Odum's theory, we propose a functional definition of carrying capacity: the upper limit of biomass that can be supported by a set primary production and within a variable food web structure is reached when total system respiration equals the sum of primary production and detrit.
Nairn , Townscape and the Campaign Against Subtopia Lorenza Pavesi

The Townscape movement had a strong influence in the British academic and professional circles. Ian Nairn was one of its early and most important advocates, particularly due to his writings for the influencial magazine Architectural Review and his TV shows. In this article based on her master’s thesis, Lorenza Pavesi discusses Nairn’s importance for planning and urban design. Lorenza is currently a visiting researcher at CPR, studying the diffusion of Townscape principles in the US, Italy, and Brazil towards her PhD with the University of São Paulo, Brazil.