Miracle-dz/UniFAR-FTUs huggingface dataset:
Disturbance and recovery following catastrophic grazing: studies of a successional chronosequence in a seagrass bed

In August 1997, a large aggregation of the common sea urchin, Lytechinus variegatus, was discovered moving southward through a lush and productive seagrass monoculture of Syringodium filiforme in the Florida Keys, FL. Sea urchin densities at the grazing front were greater than 300 individuals m -2 which resulted in the overgrazing of seagrasses and a complete denuding of all vegetation from this area. The steady rate of the grazing front migration permitted the estimation of the time since disturbance for any point behind this grazing front allowing the use of a chronosequence approach to investigate the processes early on in succession of these communities. In May 1999, six north-south parallel transects were established across the disturbed seagrass communities and into the undisturbed areas south of the grazing front. Based on the measured rates of the migration of the grazing front, we grouped 60 sites into five categories (disturbed, recently grazed, active grazing front, stressed and undisturbed). The large scale loss of seagrass biomass initiated community-wide cascading effects that significantly altered resource regimes and species diversity. The loss of the seagrass canopy and subsequent death and decay of the below-ground biomass resulted in a de-stabilization of the sediments. As the sediments were eroded into the water column, turbidity significantly increased, reducing light availability and significantly reducing the sediment nitrogen pool and depleting the seed bank. The portion of the chronosequence that has had the longest period of recovery now consists of a mixed community of seagrass and macroalgae, as remnant survivors and quick colonizers coexist and jointly take advantage of the open space.
Higher carbohydrate intake is associated with increased risk of all‐cause and disease‐specific mortality in head and neck cancer patients: results from a prospective cohort study

No studies have evaluated associations between carbohydrate intake and head and neck squamous cell carcinoma (HNSCC) prognosis. We prospectively examined associations between pre‐ and post‐treatment carbohydrate intake and recurrence, all‐cause mortality, and HNSCC‐specific mortality in a cohort of 414 newly diagnosed HNSCC patients. All participants completed pre‐ and post‐treatment Food Frequency Questionnaires (FFQs) and epidemiologic surveys. Recurrence and mortality events were collected annually. Multivariable Cox Proportional Hazards models tested associations between carbohydrate intake (categorized into low, medium and high intake) and time to recurrence and mortality, adjusting for relevant covariates. During the study period, there were 70 deaths and 72 recurrences. In pretreatment analyses, high intakes of total carbohydrate (HR: 2.29; 95% CI: 1.23–4.25), total sugar (HR: 3.03; 95% CI: 1.12–3.68), glycemic load (HR: 2.10; 95% CI: 1.15–3.83) and simple carbohydrates (HR 2.26; 95% CI 1.19–4.32) were associated with significantly increased risk of all‐cause mortality compared to low intake. High intakes of carbohydrate (HR 2.45; 95% CI: 1.23–4.25) and total sugar (HR 3.03; 95% CI 1.12–3.68) were associated with increased risk of HNSCC‐specific mortality. In post‐treatment analyses, medium fat intake was significantly associated with reduced risk of recurrence (HR 0.08; 95% CI 0.01–0.69) and all‐cause mortality (HR 0.27; 95% CI 0.07–0.96). Stratification by tumor site and cancer stage in pretreatment analyses suggested effect modification by these factors. Our data suggest high pretreatment carbohydrate intake may be associated with adverse prognosis in HNSCC patients. Clinical intervention trials to further examine this hypothesis are warranted.
Low Weight, Morbidity, and Mortality in Children With Cerebral Palsy: New Clinical Growth Charts

OBJECTIVE: To determine the percentiles of weight for age in cerebral palsy according to gender and Gross Motor Function Classification System (GMFCS) level and to identify weights associated with negative health outcomes. PATIENTS AND METHODS: This study consists of a total of 102 163 measurements of weight from 25 545 children with cerebral palsy who were clients of the California Department of Developmental Services from 1988 through 2002. Percentiles were estimated using generalized additive models for location, scale, and shape. Numbers of comorbidities were compared using t tests. The effect of low weight on mortality was estimated with proportional hazards regression. RESULTS: Weight-for-age percentiles in children with cerebral palsy varied with gender and GMFCS level. Comorbidities were more common among those with weights below the 20th percentile in GMFCS levels I through IV and level V without feeding tubes (P < .01). For GMFCS levels I and II, weights below the 5th percentile were associated with a hazard ratio of 2.2 (95% confidence interval: 1.3–3.7). For children in GMFCS levels III through V, weights below the 20th percentile were associated with a mortality hazard ratio of 1.5 (95% confidence interval: 1.4–1.7). CONCLUSIONS: Children with cerebral palsy who have very low weights have more major medical conditions and are at increased risk of death. The weight-for-age charts presented here may assist in the early detection of nutritional issues or other health risks in these children.
The role of platelet parameters as a biomarker in the diagnosis and in predicting the severity of preeclampsia

Aim: To compare platelet count, mean platelet volume and platelet distribution width in preeclampsia and normal pregnant females in diagnosis and assessing the severity preeclampsia. Materials and Methods: Case control study comprising of 50 preeclamptic females between 20 to 24 weeks of gestation as cases and 50 normotensive pregnant females matched for age and gestation as controls. Preeclamptic patients were separated into three groups as mild (25), moderate (13) and severe preeclampsia (12). Platelet count, mean platelet volume and platelet distribution width measured by automated hematology analyzer sysmex KX 21 was recorded in all the groups and analyzed. Results: Platelet count decreased significantly in patients with preeclampsia as compared to normotensive healthy females. (Mean platelet count in lakhs/cumm ± SD - 1.6688 ±.71890 vs 2.5888 ±.66881, p < 0.0001) Among preeclamptic patients there was significant decrease in platelet count with the increasing severity (mild, moderate and severe preeclampsia - 2.2044 + 0.594, 1.176 + 0.267, 1.0917 + 0.385, p < 0.0001). There was significant increase in PDW in preeclampsia when compared to normotensive pregnant females. (PDW in fl - 15.488 ± 2.4685, 11.755 ± 1.4206, p < 0.0001) There were no significant differences in MPV in normal and preeclampsia and between severities of preeclampsia. Conclusion: Platelet count emerges as a reliable indicator for diagnosing preeclampsia and predicting the severity of disease. Though, PDW is also another reliable marker for diagnosis of preeclampsia, its role in assessing the severity of preeclampsia need to be explored. Also increased MPV is not a significant predictor of preeclampsia in pregnancy. Key Words: Preeclampsia, Mean platelet volume, Platelet distribution width, Platelet count
Improving Music Structure Segmentation using lag-priors

Methods for music structure discovery usually process a music track by first detecting segments and then labeling them. Depending on the assumptions made on the signal content (repetition, homogeneity or novelty), different methods are used for these two steps. In this paper, we deal with the segmentation in the case of repetitive content. In this field, segments are usually identified by looking for sub-diagonals in a Self-Similarity-Matrix (SSM). In order to make this identification more robust, Goto proposed in 2003 to cumulate the values of the SSM over constant-lag and search only for segments in the SSM when this sum is large. Since the various repetitions of a segment start simultaneously in a self-similarity-matrix, Serra et al. proposed in 2012 to cumulate these simultaneous values (using a so-called structure feature) to enhance the novelty of the starting and ending time of a segment. In this work, we propose to combine both approaches by using Goto method locally as a prior to the lag-dimensions of Serra et al. structure features used to compute the novelty curve. Through a large experiment on RWC and Isophonics testsets and using MIREX segmentation evaluation measure, we show that this simple combination allows a large improvement of the segmentation results.
Anticipatory Adjustments to Being Picked Up in Infancy

Anticipation of the actions of others is often used as a measure of action understanding in infancy. In contrast to studies of action understanding which set infants up as observers of actions directed elsewhere, in the present study we explored anticipatory postural adjustments made by infants to one of the most common adult actions directed to them – picking them up. We observed infant behavioural changes and recorded their postural shifts on a pressure mat in three phases: (i) a prior Chat phase, (ii) from the onset of Approach of the mother’s arms, and (iii) from the onset of Contact. In Study 1, eighteen 3-month-old infants showed systematic global postural changes during Approach and Contact, but not during Chat. There was an increase in specific adjustments of the arms (widening or raising) and legs (stiffening and extending or tucking up) during Approach and a decrease in thrashing/general movements during Contact. Shifts in postural stability were evident immediately after onset of Approach and more slowly after Contact, with no regular shifts during Chat. In Study 2 we followed ten infants at 2, 3 and 4 months of age. Anticipatory behavioural adjustments during Approach were present at all ages, but with greater differentiation from a prior Chat phase only at 3 and 4 months. Global postural shifts were also more phase differentiated in older infants. Moreover, there was significantly greater gaze to the mother’s hands during Approach at 4 months. Early anticipatory adjustments to being picked up suggest that infants’ awareness of actions directed to the self may occur earlier than of those directed elsewhere, and thus enable infants’ active participation in joint actions from early in life.
Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65

RPE65 is the essential trans-cis isomerase of the classical retinoid (visual) cycle. Mutations in RPE65 give rise to severe retinal dystrophies, most of which are associated with loss of protein function and recessive inheritance. The only known exception is a c.1430G>A (D477G) mutation that gives rise to dominant retinitis pigmentosa with delayed onset and choroidal and macular involvement. Position 477 is distant from functionally critical regions of RPE65. Hence, the mechanism of D477G pathogenicity remains unclear, although protein misfolding and aggregation mechanisms have been suggested. We characterized a D477G knock-in mouse model which exhibited mild age-dependent changes in retinal structure and function. Immunoblot analysis of protein extracts from the eyes of these knock-in mice demonstrated the presence of ubiquitinated RPE65 and reduced RPE65 expression. We observed an accumulation of retinyl esters in the knock-in mice as well as a delay in rhodopsin regeneration kinetics and diminished electroretinography responses, indicative of RPE65 functional impairment induced by the D477G mutation in vivo. However, a cell line expressing D477G RPE65 revealed protein expression levels, cellular localization and retinoid isomerase activity comparable to cells expressing wild-type protein. Structural analysis of an RPE65 chimera suggested that the D477G mutation does not perturb protein folding or tertiary structure. Instead, the mutation generates an aggregation-prone surface that could induce cellular toxicity through abnormal complex formation as suggested by crystal packing analysis. These results indicate that a toxic gain-of-function induced by the D477G RPE65 substitution may play a role in the pathogenesis of this form of dominant retinitis pigmentosa.
The prognostic effect of neoadjuvant chemoradiotherapy on the change of PD-L1 expression in patients with locally advanced rectal adenocarcinoma.

PURPOSE To evaluate the prognostic effect of neoadjuvant chemoradiotherapy on the change of programmed death ligand 1 (PD-L1) expression in patients with locally advanced rectal adenocarcinoma, by comparing PD-L1 expression in pretreatment biopsies and PD-L1 expression in pathological specimens after neoadjuvant chemoradiotherapy. METHODS A total of 25 patients with rectal adenocarcinoma were evaluated. Patients were treated by neoadjuvant chemoradiotherapy (radiotherapy:44Gy normofraxionation; chemotherapy: capecitabine 825 mg/m2 in two daily doses). Surgery was performed 6-8 weeks after the chemoradiotherapy completion. PD-L1 expression was determined in endoscopic biopsies and in resected specimens with immunohistochemistry. RESULTS All 25 patients received radiotherapy without interruption, while concomitant chemotherapy was discontinued prematurely in one patient because of hematological toxicity. In 13 patients sphincter-saving surgery were performed, and 12 patients underwent rectum resection. Downstaging was noticed in 17 patients. Stable disease was found in 5 patients, and progression in 3. The median disease free survival (DFS) was not reached. Three-year DFS was 54.3% (95% CI 34.3-74.2). The median overall survival (OS) was 60 months (95% CI 48-60). Three-year OS was 75 % (95% CI 57.7-92.3). No PD-L1 expression was noticed in pretreatment biopsy and in resected tissue after chemoradiotherapy. CONCLUSION No prognostic effect of neoadjuvant chemoradiotherapy on the change of PD-L1 expression was demonstrated in patients with locally advanced rectal adenocarcinoma.
College cafeteria snack food purchases become less healthy with each passing week of the semester

Abstract Objective Snacks, stress and parties all contribute to the weight gain – the elusive ‘Freshman 15’ – that some college-goers unfortunately experience. The present study examines how à la carte snack choice changes on a university campus during each progressing week of the academic calendar. Design How à la carte snack choices change on a university campus with each progressing week of the academic calendar was examined. Setting The data were collected from three large cafeterias (or dining halls) on Cornell University's campus during four semesters (Fall 2006, Spring 2007, Fall 2007 and Spring 2008), for 18 weeks in each semester. Subjects After the à la carte snack items were divided into healthy snacks and unhealthy snacks, the percentage share for each food category was calculated. Results Within each semester, the unhealthy snack food choices increased consistently by 0·4 % per week (β = 0·00418, P < 0·01). Furthermore, a sharp (8 %) increase occurred in the final two weeks of the semester. In contrast, healthy snack food choices decreased by almost 4 % (β = −0·0408, P < 0·01) in the final two weeks during the fall semester. Conclusions These results demonstrate an increased demand for hedonic, or unhealthy, snack foods as the college semester progresses and in particular at the very end of the semester. To counter this tendency towards unhealthy snacking, cafeterias and stores should make extra effort to promote healthy alternatives during the later weeks of the semester.
A systematic review and meta-analysis

Background: Randomized trials and meta-analyses demonstrated that chronic total occlusion (CTO) in noninfarct related artery (n-IRA) was associated with increased all-cause mortality. Recently, several observational studies suggested that the successful revascularization of n-IRA with CTO decreased all-cause mortality. Methods: A systematic search was performed in Cochrane Controlled Trials Registry, PubMed, MEDLINE, and EMBASE databases for relevant studies. Article assessing the prognostic role of revascularization of n-IRA with CTO was enrolled in this metaanalysis. Data and characteristics of each study were extracted. A meta-analysis was performed to generate pooled odds ratio (OR) and 95% confidence intervals (95% CIs) for outcomes. The primary outcome was major adverse cardiac events (MACE). Beg funnel plot was used to evaluate publication bias. Results: Four observational studies and one randomized controlled trial involving 1083 patients were enrolled for analysis. Compared with nonreperfusion, the successful percutaneous coronary intervention (PCI) of n-IRA with CTO was related to decreased all-cause mortality (OR was 0.34, and 95% CI was 0.2–0.59; P= .0001). Conclusions: Successful PCI of n-IRA with CTO could significantly decrease all-cause mortality, cardiac mortality, MACE, and stroke in acute myocardial infarction patients. In addition, it was not associated with the increased risk of repeat revascularization and myocardial infarction. Abbreviations: ACS= acute coronary syndrome, AMI = acute myocardial infarction, CTO = chronic total occlusion, LVEDV = left ventricular end diastolic volume, LVEF = left ventricular ejection fraction, MACE =major adverse cardiac events, MVD =multivessel disease, n-IRA = noninfarct related artery, PCI = percutaneous coronary intervention, PTCA = percutaneous transluminal coronary angioplasty, STEMI = ST-segment elevation myocardial infarction, SVD = single vessel disease.
Distributive Lattices

Morphisms. Let A and B be involutive lattices. A morphism from A to B is a function h : A → B that is a homomorphism: h(x ∨ y) = h(x) ∨ h(y), h(x ∨ y) = h(x) ∧ h(y), h(x → y) = h(x) → h(y)
The metabolic fate of the amido-N group of glutamine in the tissues of the gastrointestinal tract in 24 h-fasted sheep

Whole-body and gastrointestinal tract (GIT) metabolism of [5-15N]glutamine were monitored in lambs (33 kg live weight) fasted for 24 h. Animals were previously prepared with vascular catheters across the mesenteric-(MDV) and portal-drained viscera (PDV) to permit quantification of mass and isotopic transfers of metabolites by arterio-venous difference. Continuous infusions of [5-15N]glutamine into the jugular vein were conducted for 10 h and integrated blood samples withdrawn over 75 min intervals for the last 5 h of infusion. The lambs were then killed and portions from various tissues of the digestive tract and other body organs removed for determination of 15N enrichment in RNA, DNA and protein (the latter obtained by difference using total acid-precipitable N). Whole-body glutamine flux was 108 μmol/min of which 23 and 47 % could be attributed to MDV and PDV metabolism (P < 0·001) respectively. There was a small net production of glutamine across the MDV. GIT blood-flows and NH3 production were partitioned 3:2 between MDV and non-MDV components. Less than 5 % of the NH3 produced was derived from the amido-N of glutamine, while across the small intestine (MDV) 26 % of the glutamine flux was converted to NH3, compared with 18 % for non-MDV transfers. The 15N enrichments in protein were of the order jejunum > duodenum > ileum with mucosal cells more labelled than serosal (P < 0·001). Lesser enrichments were observed for other GIT tissues (abomasum > caecum > rumen) while liver and lymph were comparable with the abomasum; kidney, spleen and muscle were lower still (P < 0·05). Enrichments of RNA were similar to that of protein and followed the same pattern, except for higher relative values for liver, spleen and lymphoid tissue. The lowest enrichments were observed for DNA, but again the pattern order was similar except for increased label in lymph, caecum and the spleen. For the MDV there was reasonable agreement between 15N-disappearance as glutamine and appearance in NH3 (24 %), protein (81 %), RNA (3·6 %) and DNA (2·1 %). For the total PDV there was a shortfall (−12 %), however, which may be due to losses in lumen components. These results show the importance of the GIT as a contributor to total glutamine plasma flux, but indicate a lesser reliance on glutamine metabolism by the digestive tract of the ruminant compared with observations from non-ruminants.
Sublethal Behavioral and Physiological Effects of the Biomedical Bleeding Process on the American Horseshoe Crab, Limulus polyphemus

The hemolymph of the American horseshoe crab, Limulus polyphemus, is harvested from over 500,000 animals annually to produce Limulus amebocyte lysate (LAL), a medically important product used to detect pathogenic bacteria. Declining abundance of spawning Limulus females in heavily harvested regions suggests deleterious effects of this activity, and while mortality rates of the harvest process are known to be 10%–30%, sublethal behavioral and physiological effects are not known. In this study, we determined the impact of the harvest process on locomotion and hemocyanin levels of 28 female horseshoe crabs. While mortality rates after bleeding (18%) were similar to previous studies, we found significant decreases in the linear and angular velocity of freely moving animals, as well as changes in their activity levels and expression of circatidal behavioral rhythms. Further, we found reductions in hemocyanin levels, which may alter immune function and cuticle integrity. These previously unrecognized behavioral and physiological deficits suggest that the harvest of LAL may decrease female fitness, and thus may contribute to the current population decline.
Heat Transfer Enhancement due to Acoustic Fields: A Methodological Analysis

The aim of this paper is to expose the main involved physical phenomena underlying the alteration of convective heat transfer in a heat exchanger subjected to imposed vibrations. This technique seems to have interesting features and industrial applications, such as for efficiency increases, heat transfer rate control and cleanliness action. However, a clear description and comprehension of how vibrations may alter the convective heat transfer coefficient in a heat exchanger has still not been reached due to the complexity of the involved physical mechanisms. For this reason, after a presentation and a schematization of the analyzed thermodynamic system, the fundamental alterations of the thermo-fluid dynamics fields are described. Then, the main involved physical phenomena are exposed for the three cases of gaseous, monophasic liquid and boiling liquid mediums. Finally, on the basis of the characteristics of these described phenomena, some considerations and indications of general validity are presented.