Ecological-niche factor analysis: how to compute habitat-suitability maps without absence data?

We propose a multivariate approach to the study of geographic species distribution which does not require absence data. Building on Hutchinson's concept of the ecological niche, this factor analysis compares, in the multidimensional space of ecological variables, the distribution of the localities where the focal species was observed to a reference set describing the whole study area. The first factor extracted maximizes the marginality of the focal species, defined as the ecological distance between the species optimum and the mean habitat within the reference area. The other factors maximize the specialization of this focal species, defined as the ratio of the ecological variance in mean habitat to that observed for the focal species. Eigenvectors and eigenvalues are readily interpreted and can be used to build habitat-suitability maps. This approach is recommended in Situations where absence data are not available (many data banks), unreliable (most cryptic or rare species), or meaningless (invaders). We provide an illustration and validation of the method for the alpine ibex, a species reintroduced in Switzerland which presumably has not yet recolonized its entire range.

Energy deficit and length of hospital stay can be reduced by a two-step quality improvement of nutrition therapy: the intensive care unit dietitian can make the difference.

OBJECTIVE: Critically ill patients are at high risk of malnutrition. Insufficient nutritional support still remains a widespread problem despite guidelines. The aim of this study was to measure the clinical impact of a two-step interdisciplinary quality nutrition program. DESIGN: Prospective interventional study over three periods (A, baseline; B and C, intervention periods). SETTING: Mixed intensive care unit within a university hospital. PATIENTS: Five hundred seventy-two patients (age 59 ± 17 yrs) requiring >72 hrs of intensive care unit treatment. INTERVENTION: Two-step quality program: 1) bottom-up implementation of feeding guideline; and 2) additional presence of an intensive care unit dietitian. The nutrition protocol was based on the European guidelines. MEASUREMENTS AND MAIN RESULTS: Anthropometric data, intensive care unit severity scores, energy delivery, and cumulated energy balance (daily, day 7, and discharge), feeding route (enteral, parenteral, combined, none-oral), length of intensive care unit and hospital stay, and mortality were collected. Altogether 5800 intensive care unit days were analyzed. Patients in period A were healthier with lower Simplified Acute Physiologic Scale and proportion of "rapidly fatal" McCabe scores. Energy delivery and balance increased gradually: impact was particularly marked on cumulated energy deficit on day 7 which improved from -5870 kcal to -3950 kcal (p < .001). Feeding technique changed significantly with progressive increase of days with nutrition therapy (A: 59% days, B: 69%, C: 71%, p < .001), use of enteral nutrition increased from A to B (stable in C), and days on combined and parenteral nutrition increased progressively. Oral energy intakes were low (mean: 385 kcal*day, 6 kcal*kg*day ). Hospital mortality increased with severity of condition in periods B and C. CONCLUSION: A bottom-up protocol improved nutritional support. The presence of the intensive care unit dietitian provided significant additional progression, which were related to early introduction and route of feeding, and which achieved overall better early energy balance.

Thermogenesis in obese women: effect of fructose vs. glucose added to a meal.

To assess the effect of a fructose meal on resting energy expenditure (EE), indirect calorimetry was used in 23 women (10 lean and 13 obese) for 30 min before and 6 h after the ingestion of a mixed meal containing 20% protein, 33% fat, and either 75 g glucose or 75 g fructose as carbohydrate source (47%). Expressed as a percentage of the energy content of the meal, the thermogenic response to the fructose meal was significantly greater (10.2 +/- 0.5%) than that of the glucose meal (8.4 +/- 0.4%, P less than 0.01). This difference was still apparent when the lean and obese women were considered separately. The mean respiratory quotient during the 6-h postprandial period was significantly greater (P less than 0.01) for the fructose (0.85 +/- 0.01) than for the glucose meal (0.83 +/- 0.01) in the combined subjects. In addition, cumulative carbohydrate oxidation was significantly greater after the fructose than after the glucose meal (51.1 +/- 2.3 vs. 40.9 +/- 2.0 g/6 h, respectively, P less than 0.01). Only small changes were observed in postprandial plasma levels of glucose and insulin after the fructose meal, but the plasma levels of lactate increased more with fructose than with the glucose meal. These results suggest that there might be some advantages (higher thermogenesis and carbohydrate oxidations) in using fructose as part of the carbohydrate source in diet of people with obesity and/or insulin resistance.

Illite "crystallinity'' revisited

The Kubler Index (KI) is defined as the full width at half-maximum height (FWHM) of the 10-Angstrom X-ray diffraction peak of illite-smectite interstratified (I-S) clay minerals, The only parameters controlling the Kubler index are assumed to be the mean number of layers (N) in the coherent scattering domains (CSD). the variance of the distribution of the number of layers of the CSB, the mean percentage of smectite layers in I-S (%S), and the probability of layer stocking (Reichweite). The Kubler-Index measurements on ah-dried (KIAD) and ethylene-glycolated (KIEG) samples were compared to N and %S using the NEWMOD computer program to simulate X-ray diffraction patterns. Charts of KIAD versus KIEG corrected for instrumental broadening were made and isolines were mapped for constant N and CLS. Isolines allow a direct and rapid determination of N and RS from KI measurements. The method allows quantification of the metamorphic anchizone limits by considering mean thickness of fundamental particles in MacEwan crystallites. The transition from diagenesis to the anchizone and from the anchizone to the epizone of low-grade metamorphism corresponds to thicknesses of 20- and 70-layer fundamental particles, respectively.

Validation of the spiritual distress assessment tool in older hospitalized patients.

ABSTRACT:¦BACKGROUND: The Spiritual Distress Assessment Tool (SDAT) is a 5-item instrument developed to assess unmet spiritual needs in hospitalized elderly patients and to determine the presence of spiritual distress. The objective of this study was to investigate the SDAT psychometric properties.¦METHODS: This cross-sectional study was performed in a Geriatric Rehabilitation Unit. Patients (N = 203), aged 65 years and over with Mini Mental State Exam score ≥ 20, were consecutively enrolled over a 6-month period. Data on health, functional, cognitive, affective and spiritual status were collected upon admission. Interviews using the SDAT (score from 0 to 15, higher scores indicating higher distress) were conducted by a trained chaplain. Factor analysis, measures of internal consistency (inter-item and item-to-total correlations, Cronbach α), and reliability (intra-rater and inter-rater) were performed. Criterion-related validity was assessed using the Functional Assessment of Chronic Illness Therapy-Spiritual well-being (FACIT-Sp) and the question "Are you at peace?" as criterion-standard. Concurrent and predictive validity were assessed using the Geriatric Depression Scale (GDS), occurrence of a family meeting, hospital length of stay (LOS) and destination at discharge.¦RESULTS: SDAT scores ranged from 1 to 11 (mean 5.6 ± 2.4). Overall, 65.0% (132/203) of the patients reported some spiritual distress on SDAT total score and 22.2% (45/203) reported at least one severe unmet spiritual need. A two-factor solution explained 60% of the variance. Inter-item correlations ranged from 0.11 to 0.41 (eight out of ten with P < 0.05). Item-to-total correlations ranged from 0.57 to 0.66 (all P < 0.001). Cronbach α was acceptable (0.60). Intra-rater and inter-rater reliabilities were high (Intraclass Correlation Coefficients ranging from 0.87 to 0.96). SDAT correlated significantly with the FACIT-Sp, "Are you at peace?", GDS (Rho -0.45, -0.33, and 0.43, respectively, all P < .001), and LOS (Rho 0.15, P = .03). Compared with patients showing no severely unmet spiritual need, patients with at least one severe unmet spiritual need had higher odds of occurrence of a family meeting (adjOR 4.7, 95%CI 1.4-16.3, P = .02) and were more often discharged to a nursing home (13.3% vs 3.8%; P = .027).¦CONCLUSIONS: SDAT has acceptable psychometrics properties and appears to be a valid and reliable instrument to assess spiritual distress in elderly hospitalized patients.

How do gastroenterologists assess overall activity of eosinophilic esophagitis in adult patients?

OBJECTIVES: There is no "gold standard" for assessing disease activity in patients with eosinophilic esophagitis (EoE). We aimed to compare physicians' judgment of EoE activity with patients' judgment of symptom severity. We also aimed to examine the relative contribution of symptoms as well as endoscopic and histologic findings in shaping physicians' judgment of EoE activity. METHODS: Six gastroenterologists (all EoE experts) assessed EoE-associated symptoms in adult patients. Patients completed a symptom instrument and provided global assessment of EoE symptom severity (PatGA) (Likert scale: 0 (inactive) to 10 (most active)). Following esophagogastroduodenoscopy with biopsy sampling, gastroenterologists provided a global assessment of EoE activity (PhysGA) (Likert scale from 0 to 10) based on patient history and endoscopic and histologic findings. Linear regression and analysis of variance was used to quantify the extent to which variations in severity of EoE symptoms and endoscopic and histologic findings explain variations in PhysGA. RESULTS: A total of 149 EoE patients were prospectively included (71.8% male, median age at inclusion 38 years, 71.8% with concomitant allergies). A moderate positive correlation between PhysGA and PatGA (rho=0.442, P<0.001) was observed and the mean difference in the Bland-Altman plot was 1.77. Variations in severity of endoscopic findings, symptoms, and histologic findings alone explained 53%, 49%, and 30%, of the variability in PhysGA, respectively. Together, these findings explained 75% of variability in PhysGA. CONCLUSIONS: Gastroenterologists rate EoE activity mainly on the basis of endoscopic findings and symptoms and, to a lesser extent, on histologic findings.

The use of beta-blockers is associated with the occurrence of acute kidney injury in severe alcoholic hepatitis.

BACKGROUND & AIMS: The beneficial effect of nonselective beta-blockers (NSBB) has recently been questioned in patients with end-stage cirrhosis. We analysed the impact of NSBB on outcomes in severe alcoholic hepatitis (AH). METHODS: This study was based on a prospective database of patients with severe, biopsy-proven AH. Patients admitted from July, 2006 to July, 2014 were retrospectively studied. Patients were divided into two groups (with and without NSBB) and assessed for the occurrence of Acute Kidney Injury (AKI) and transplant-free mortality during a 168-day follow-up period. RESULTS: One hundred thirty-nine patients were included, the mean Maddrey score was 71 ± 34 and 86 patients (61.9%) developed AKI. Forty-eight patients (34.5%) received NSBB. The overall 168-day transplant-free mortality was 50.5% (95%CI, 41.3-60.0%). The overall 168-day cumulative incidence of AKI was 61.9% (95%CI, 53.2-69.4%). When compared, patients with NSBB had a lower heart rate (65 ± 13 vs 92 ± 12, P < 0.0001) and a lower mean arterial pressure (MAP, 78 ± 3 vs 87 ± 5, P < 0.0001). Patients with NSBB had comparable MELD scores, Maddrey scores, and medical histories. The 168-day transplant-free mortality was 56.8% (95%CI, 41.3-69.7%) in patients with NSBB and 46.7% (95%CI, 35.0-57.6%) without NSBB (P = 0.25). The 168-day cumulative incidence of AKI was 89.6% (95%CI, 74.9-95.9%) with NSBB compared to 50.4% (95%CI: 39.0-60.7) for no NSBB (P = 0.0001). The independent factors predicting AKI were a higher MELD score and the presence of NSBB. CONCLUSIONS: The use of NSBB in patients with severe AH is independently associated with a higher cumulative incidence of AKI.

Does phylogeographic structure relate to climatic niche divergence? A test using maritime pine (Pinus pinaster Ait.)

Aim To disentangle the effects of environmental and geographical processes driving phylogenetic distances among clades of maritime pine (Pinus pinaster). To assess the implications for conservation management of combining molecular information with species distribution models (SDMs; which predict species distribution based on known occurrence records and on environmental variables). Location Western Mediterranean Basin and European Atlantic coast. Methods We undertook two cluster analyses for eight genetically defined pine clades based on climatic niche and genetic similarities. We assessed niche similarity by means of a principal component analysis and Schoener's D metric. To calculate genetic similarity, we used the unweighted pair group method with arithmetic mean based on Nei's distance using 266 single nucleotide polymorphisms. We then assessed the contribution of environmental and geographical distances to phylogenetic distance by means of Mantel regression with variance partitioning. Finally, we compared the projection obtained from SDMs fitted from the species level (SDMsp) and composed from the eight clade-level models (SDMcm). Results Genetically and environmentally defined clusters were identical. Environmental and geographical distances explained 12.6% of the phylogenetic distance variation and, overall, geographical and environmental overlap among clades was low. Large differences were detected between SDMsp and SDMcm (57.75% of disagreement in the areas predicted as suitable). Main conclusions The genetic structure within the maritime pine subspecies complex is primarily a consequence of its demographic history, as seen by the high proportion of unexplained variation in phylogenetic distances. Nevertheless, our results highlight the contribution of local environmental adaptation in shaping the lower-order, phylogeographical distribution patterns and spatial genetic structure of maritime pine: (1) genetically and environmentally defined clusters are consistent, and (2) environment, rather than geography, explained a higher proportion of variation in phylogenetic distance. SDMs, key tools in conservation management, better characterize the fundamental niche of the species when they include molecular information.

What Role Does Sleep Play in Weight Gain in the First Semester of University?

We hypothesized that shorter sleep durations and greater variability in sleep patterns are associated with weight gain in the first semester of university. Students (N = 132) completed daily sleep diaries for 9 weeks, completed the MEQ (chronotype) and CES-D (depressed mood) at week 9, and self-reported weight/height (weeks 1 & 9). Mean and variability scores were calculated for sleep duration (TST, TSTv), bedtime (BT, BTv), and wake time (WT, WTv). An initial hierarchical regression evaluated (block 1) sex, ethnicity; (block 2) depressed mood, chronotype; (block 3) TST; (block 4) BT, WT; and (block 5; R(2) change = 0.09, p = 0.005) TSTv, BTv, WTv with weight change. A sex-by-TSTv interaction was found. A final model showed that ethnicity, TST, TSTv, and BTv accounted for 31% of the variance in weight change for males; TSTv was the most significant contributor (R(2) change = 0.21, p < 0.001). Daily variability in sleep duration contributes to males' weight gain. Further investigation needs to examine sex-specific outcomes for sleep and weight.

Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities.

IMPORTANCE: The 16p11.2 BP4-BP5 duplication is the copy number variant most frequently associated with autism spectrum disorder (ASD), schizophrenia, and comorbidities such as decreased body mass index (BMI). OBJECTIVES: To characterize the effects of the 16p11.2 duplication on cognitive, behavioral, medical, and anthropometric traits and to understand the specificity of these effects by systematically comparing results in duplication carriers and reciprocal deletion carriers, who are also at risk for ASD. DESIGN, SETTING, AND PARTICIPANTS: This international cohort study of 1006 study participants compared 270 duplication carriers with their 102 intrafamilial control individuals, 390 reciprocal deletion carriers, and 244 deletion controls from European and North American cohorts. Data were collected from August 1, 2010, to May 31, 2015 and analyzed from January 1 to August 14, 2015. Linear mixed models were used to estimate the effect of the duplication and deletion on clinical traits by comparison with noncarrier relatives. MAIN OUTCOMES AND MEASURES: Findings on the Full-Scale IQ (FSIQ), Nonverbal IQ, and Verbal IQ; the presence of ASD or other DSM-IV diagnoses; BMI; head circumference; and medical data. RESULTS: Among the 1006 study participants, the duplication was associated with a mean FSIQ score that was lower by 26.3 points between proband carriers and noncarrier relatives and a lower mean FSIQ score (16.2-11.4 points) in nonproband carriers. The mean overall effect of the deletion was similar (-22.1 points; P < .001). However, broad variation in FSIQ was found, with a 19.4- and 2.0-fold increase in the proportion of FSIQ scores that were very low (≤40) and higher than the mean (>100) compared with the deletion group (P < .001). Parental FSIQ predicted part of this variation (approximately 36.0% in hereditary probands). Although the frequency of ASD was similar in deletion and duplication proband carriers (16.0% and 20.0%, respectively), the FSIQ was significantly lower (by 26.3 points) in the duplication probands with ASD. There also were lower head circumference and BMI measurements among duplication carriers, which is consistent with the findings of previous studies. CONCLUSIONS AND RELEVANCE: The mean effect of the duplication on cognition is similar to that of the reciprocal deletion, but the variance in the duplication is significantly higher, with severe and mild subgroups not observed with the deletion. These results suggest that additional genetic and familial factors contribute to this variability. Additional studies will be necessary to characterize the predictors of cognitive deficits.

Sociodemographic, behavioral and genetic determinants of allostatic load in a Swiss population-based study.

Allostatic load (AL) is a marker of physiological dysregulation which reflects exposure to chronic stress. High AL has been related to poorer health outcomes including mortality. We examine here the association of socioeconomic and lifestyle factors with AL. Additionally, we investigate the extent to which AL is genetically determined. We included 803 participants (52% women, mean age 48±16years) from a population and family-based Swiss study. We computed an AL index aggregating 14 markers from cardiovascular, metabolic, lipidic, oxidative, hypothalamus-pituitary-adrenal and inflammatory homeostatic axes. Education and occupational position were used as indicators of socioeconomic status. Marital status, stress, alcohol intake, smoking, dietary patterns and physical activity were considered as lifestyle factors. Heritability of AL was estimated by maximum likelihood. Women with a low occupational position had higher AL (low vs. high OR=3.99, 95%CI [1.22;13.05]), while the opposite was observed for men (middle vs. high OR=0.48, 95%CI [0.23;0.99]). Education tended to be inversely associated with AL in both sexes(low vs. high OR=3.54, 95%CI [1.69;7.4]/OR=1.59, 95%CI [0.88;2.90] in women/men). Heavy drinking men as well as women abstaining from alcohol had higher AL than moderate drinkers. Physical activity was protective against AL while high salt intake was related to increased AL risk. The heritability of AL was estimated to be 29.5% ±7.9%. Our results suggest that generalized physiological dysregulation, as measured by AL, is determined by both environmental and genetic factors. The genetic contribution to AL remains modest when compared to the environmental component, which explains approximately 70% of the phenotypic variance.

Equating accelerometer estimates among youth: The Rosetta Stone 2.

OBJECTIVES: Different accelerometer cutpoints used by different researchers often yields vastly different estimates of moderate-to-vigorous intensity physical activity (MVPA). This is recognized as cutpoint non-equivalence (CNE), which reduces the ability to accurately compare youth MVPA across studies. The objective of this research is to develop a cutpoint conversion system that standardizes minutes of MVPA for six different sets of published cutpoints. DESIGN: Secondary data analysis. METHODS: Data from the International Children's Accelerometer Database (ICAD; Spring 2014) consisting of 43,112 Actigraph accelerometer data files from 21 worldwide studies (children 3-18 years, 61.5% female) were used to develop prediction equations for six sets of published cutpoints. Linear and non-linear modeling, using a leave one out cross-validation technique, was employed to develop equations to convert MVPA from one set of cutpoints into another. Bland Altman plots illustrate the agreement between actual MVPA and predicted MVPA values. RESULTS: Across the total sample, mean MVPA ranged from 29.7MVPAmind(-1) (Puyau) to 126.1MVPAmind(-1) (Freedson 3 METs). Across conversion equations, median absolute percent error was 12.6% (range: 1.3 to 30.1) and the proportion of variance explained ranged from 66.7% to 99.8%. Mean difference for the best performing prediction equation (VC from EV) was -0.110mind(-1) (limits of agreement (LOA), -2.623 to 2.402). The mean difference for the worst performing prediction equation (FR3 from PY) was 34.76mind(-1) (LOA, -60.392 to 129.910). CONCLUSIONS: For six different sets of published cutpoints, the use of this equating system can assist individuals attempting to synthesize the growing body of literature on Actigraph, accelerometry-derived MVPA.