Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Rates and Probabilities of Origination and Extinction Using Taxonomic Occurrence Data : Capture ‐ Mark ‐ Recapture ( CMR ) Approaches

Introduction There are multiple programs freely available for CMR analyses, and of course it is also possible to write your own scripts in your programming language of choice for such analyses once you grasp the principles behind the approach. Here we will focus on giving a first introduction to the freely available program MARK (http://welcome.warnercnr.colostate.edu/~gwhite/mark/mark.htm and http://www.phidot.org/software/mark/index.html) which runs on Windows. MARK was developed by Gary White, and he continues to add new models and features to this program. It has a user‐friendly interface and can also be called by R. The R package that can be conveniently used in conjunction with MARK is RMark (http://www.phidot.org/software/mark/rmark/). We will not go into the mechanics of RMark here, because our aim is only to familiarize the reader with the first basics of MARK and CMR analyses. Note that there are also many MARK (and RMark) workshops organized in North America and other parts of the world. These cater mainly to population ecologists for now, so one should be a somewhat familiar with ecological jargon for full appreciation at such workshops. This short guide will hopefully help with some of the initial “translations” between ecological and paleontological jargon. Check out the next workshop at the MARK homepage (see links above) and be sure to read the freely available “Program MARK: a gentle introduction” also downloadable from the above links, after reading our short guide. This online MARK book, edited by Evan Cooch and Gary White, which we refer to as Cooch and White (2006) throughout, gives many more details on both MARK and CMR approaches than we are able to do within this space. But again, some familiarity with the ecological jargon used will illuminate how some of the models already available can be applied to paleontological questions.
Migrant threads on process farms: parallel programming with Ariadne

We present a novel and portable threads-based system for the development of concurrent applications on shared and distributed memory environments. Implementing user-space threads. the Ariadne system is highly effective for medium to coarse grained applications. Sequential programs are readily converted into parallel programs for shared ordistributed memory, with low development effort. We describe basic threads primitives, and constructs for synchronization and computation in concurrent applications. Ariadne flexibly caters to a variety of communication environments, through a simple interface. It supports the development ofcustomized schedulers on shared memory mulliprocessors, and offers a thread migration capability for distributed environments. Scheduling ofcomputations at the thread level offers both taskand data-driven executions. Thread migration is a powerful feature which turns remote memory accesses into local accesses, enables load-balancing and simplifies program development. Ariadne currently runs on the SPARe (SunGS 4.x, SunGS 5.x), Sequent Symmetry, Intel Paragon, Silicon Graphics IRIX, and ffiM RS/6000 environments. We present Ariadne's parallel programming capability through several examples, reporting on performance measurements obtained with each. • Research supponed in pan by NATO-CRG900108, ONR-9310233, and ARO-93G0045.
Morphological optimization for tensegrity quadruped locomotion

The increasing complexity of soft and hybrid-soft robots highlights the need for more efficient methods of minimizing machine learning solution spaces, and creative ways to ease the process of rapid prototyping. In this paper, we present an initial exploration of this process, using hand-chosen morphologies. Four different choices of muscle groups will be actuated on a tensegrity quadruped called MountainGoat: three for a primarily spine-driven morphology, and one for a primarily leg-driven morphology, and the locomotion speed will be compared. Each iteration of design seeks to reduce the total number of active muscles, and consequently reduce the dimensionality of the problem for machine learning, while still producing effective locomotion. The reduction in active muscles seeks to simplify future rapid prototyping of the robot.
On the Prudence of Rewarding a While Hoping for B

In multiple-task hidden-action models, the (mis-)allocation of effort may play an important role for benefit creation. Signals which capture this benefit and which are used in incentive schemes should thus not only be judged by the noise and the associated costs but also by the mis-allocation which they induce. How can mis-allocation be measured? This article presents two requirements for such a measure (invariance and monotonicity) and analyses whether they are met by proposed measures of mis-allocation. All examined measures assert that an unbiased signal for benefit leads to the lowest misallocation. Here, the signal leading to the lowest mis-allocation is computed and shown to be unbiased for the benefit only under restrictive assumptions on the cost function (equal marginal costs for different tasks). Generally, using an unbiased signal does not imply the lowest mis-allocation.
Multicomponent methods: evaluation of new and traditional soft tissue mineral models by in vivo neutron activation analysis.

BACKGROUND Practical and accurate methods for quantifying the soft tissue mineral component of multicomponent fat-estimation models are needed. OBJECTIVES The aims were to develop a new complete model for estimating soft tissue minerals based on measured total body water (TBW) and extracellular water (ECW) and a simplified new model based on TBW measurements only and to compare these estimates with those determined with 2 traditional models (ie, the Brozek and Selinger models) and with criterion estimates based on in vivo neutron activation (IVNA) analysis. DESIGN The subjects were 156 healthy adults and 50 patients with AIDS. Total body potassium, sodium, chlorine, and calcium were measured by IVNA; TBW by (3)H(2)O or D(2)O dilution; ECW by bromide dilution; and bone mineral by dual-energy X-ray absorptiometry. RESULTS The mean (+/- SD) mass of total-body soft tissue minerals in healthy adults was 467 +/- 62 g with the IVNA model, 492 +/- 62 g with the new model, and 487 +/- 59 g with the simplified new model. Compared with the IVNA model, the complete and simplified new models overestimated soft tissue minerals by 5.4% and 4.6% (both P < 0.001), respectively. In contrast, the Brozek and Selinger models overestimated overall mean soft tissue minerals by 35% and 99% (both P < 0.001), respectively. Overall results for soft tissue mineral prediction with the 2 new models were less satisfactory for the patients with AIDS, although the results were better than those with the traditional models. CONCLUSIONS The physiologically formulated complete new model for estimating soft tissue minerals provides the opportunity to upgrade the accuracy of current multicomponent models for estimating total body fat.
The Effect of Hypnosis on Adherence to Antituberculosis Drugs Using the Health Belief Model

Abstract An RCT on the efficacy of hypnosis in improving adherence to antituberculosis treatment using the Health Belief Model (HBM). Sixty study subjects were sampled at random from tuberculosis patients who visited the Center for Pulmonary Community Health in Solo, Indonesia. Hypnotherapy with posthypnotic suggestions was delivered once a week over 6 months. The data on pretested 7 HBM constructs were analyzed using t test and path analysis. Hypnotherapy had a positive effect on perceived susceptibility, seriousness, threat, benefit, and self-efficacy. It indirectly had a positive effect on adherence. Hypnotherapy had a negative effect on perceived barrier. This study supports the hypothesis that hypnotherapy effectively improves adherence to tuberculosis treatment, by enhancing health-related perception and beliefs in the HBM.
Assessing Overweight in School Going Children : A Simplified Formula

Background: The International Obesity Task Force (IOTF) has developed new cut-offs for defining overweight and obesity in children. The cut-offs have been developed for children 2-18 years of age. Objective: To develop a simplified formula for rapid assessment of overweight in school going children. Methods: We used the extended IOTF standards used for assessment of overweight and obesity among school going children. We plotted the Body Mass Index (BMI) at level 25, developed by IOTF as the cut-off for defining overweight among children, against age in months. Scatter plots and simple linear regression was used to develop a simplified formula for the relationship between age in months and the IOTF BMI cut-off for overweight. Correlation coefficients and R2 values were used to choose an appropriate simplified formula. Results: Age in months and IOTF BMI cut-offs are linearly related from age six to 18 years. The trend is more linear in boys. Girls show a more or less ‘S’ shaped relationship compared to boys where the relationship is ‘J’ shaped. The simplified formula developed has a higher correlation coefficient for boys as compared to girls. Conclusion: The simplified formula can be easily used in field settings for rapid assessment of overweight among school children, in absence of IOTF cut-offs. Further studies are warranted to estimate the validity of these formulae under field settings.
A Novel Synthesis of 4-Acetoxyl 5(4H)-Oxazolones by Direct α-Oxidation of N-Benzoyl Amino-Acid Using Hypervalent Iodine

We have developed a new method to prepare 4-acetoxy substituted 5(4H)-oxazolones by direct oxidation of N-benzoyl amino-acids using hypervalent iodine. The method is efficient, economical and easy to perform for the synthesis of quaternary substituted amino acid derivatives. We used online FTIR monitoring techniques to analyze the reaction, and gave a plausible reaction mechanism.
enetic mixed stock analysis of an interceptory Atlantic salmon shery in the Northwest Atlantic

Interceptory fisheries represent an ongoing threat to migratory fish stocks particularly when managed in the absence of stock specific catch and exploitation information. Atlantic salmon from the southern portion of the North American range may be subject to exploitation in the commercial and recreational salmon fisheries occurring in the French territorial waters surrounding St. Pierre and Miquelon off southern Newfoundland. We evaluated stock composition of Atlantic salmon harvested in the St. Pierre and Miquelon Atlantic salmon fishery using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 12,409 individuals, 12 regional groups) encompassing the species western Atlantic range. Individual salmon were sampled from the St. Pierre and Miquelon fishery over four years (2004, 2011, 2013, and 2014). Biological characteristics indicate significant variation among years in the size and age distribution. Nonetheless, estimates of stock composition of the samples showed consistent dominance of three regions (i.e., Southern Gulf of St. Lawrence, Gaspe Peninsula, and Newfoundland). Together salmon from these regions accounted for more than 70% of annual harvest over the decade examined. Comparison of individual assignments and biological characteristics revealed a trend of declining fresh water age with latitude of assigned region. Moreover, locally harvested Newfoundland salmon were ten times more likely to be small or one sea winter individuals whereas Quebec and Gaspe Peninsula salmon were two-three times more likely to be harvested as large or two sea winter salmon. Estimates of region specific catch were highest for salmon from the southern Gulf of St. Lawrence region ranging from 242 to 887 individuals annually. This work illustrates how genetic analysis of interceptory marine fisheries can directly inform assessment and management efforts in highly migratory marine
Quantitative Trait Locus and Brain Expression of HLA-DPA1 Offers Evidence of Shared Immune Alterations in Psychiatric Disorders

Genome-wide association studies of schizophrenia encompassing the major histocompatibility locus (MHC) were highly significant following genome-wide correction. This broad region implicates many genes including the MHC complex class II. Within this interval we examined the expression of two MHC II genes (HLA-DPA1 and HLA-DRB1) in brain from individual subjects with schizophrenia (SZ), bipolar disorder (BD), major depressive disorder (MDD), and controls by differential gene expression methods. A third MHC II mRNA, CD74, was studied outside of the MHC II locus, as it interacts within the same immune complex. Exon microarrays were performed in anterior cingulate cortex (ACC) in BD compared to controls, and both HLA-DPA1 and CD74 were decreased in expression in BD. The expression of HLA-DPA1 and CD74 were both reduced in hippocampus, amygdala, and dorsolateral prefrontal cortex regions in SZ and BD compared to controls by specific qPCR assay. We found several novel HLA-DPA1 mRNA variants spanning HLA-DPA1 exons 2-3-4 as suggested by exon microarrays. The intronic rs9277341 SNP was a significant cis expression quantitative trait locus (eQTL) that was associated with the total expression of HLA-DPA1 in five brain regions. A biomarker study of MHC II mRNAs was conducted in SZ, BD, MDD, and control lymphoblastic cell lines (LCL) by qPCR assay of 87 subjects. There was significantly decreased expression of HLA-DPA1 and CD74 in BD, and trends for reductions in SZ in LCLs. The discovery of multiple splicing variants in brain for HLA-DPA1 is important as the HLA-DPA1 gene is highly conserved, there are no reported splicing variants, and the functions in brain are unknown. Future work on the function and localization of MHC Class II proteins in brain will help to understand the role of alterations in neuropsychiatric disorders. The HLA-DPA1 eQTL is located within a large linkage disequilibrium block that has an irrefutable association with schizophrenia. Future tests in a larger cohort are needed to determine the significance of this eQTL association with schizophrenia. Our findings support the long-held hypothesis that alterations in immune function are associated with the pathophysiology of psychiatric disorders.
Network analysis of adhesion/growth‐regulatory galectins and their binding sites in adult chicken retina and choroid

The highly ordered multilayered organization of the adult chicken retina is a suitable test model for examining zonal distribution of the members of a bioeffector family. Based on the concept of the sugar code, the functional pairing of glycan epitopes with cognate receptors (lectins) is emerging as a means to explain the control of diverse physiological activities. Having recently completed the biochemical characterization of all seven adhesion/growth‐regulatory galectins present in chicken, it was possible to establish how the individual characteristics of their expression profiles add up to shape the galectin network, which until now has not been defined at this level of complexity. This information will also have relevance in explaining the region‐specific presence of glycan determinants in the retina, as illustrated in the first part of this study using a panel of nine plant/fungal agglutinins. The following systematic monitoring of the galectins yielded patterns for which quantitative and qualitative differences were detected. Obviously, positivity in distinct layers is not confined to a single protein of this family, e.g. CG‐1A, CG‐3 or CG‐8. These results underline the requirement for network analysis for these proteins that can functionally interact in additive or antagonistic modes. Labeling of the tissue galectins facilitated profiling of their accessible binding sites. It also revealed differences among the galectin family members, highlighting the ability of this method to define binding properties on the level of tissue sections. Methodologically, the detection of endogenous lectins intimates that cognate glycans can become inaccessible, a notable caveat for lectin histochemical studies.
Prolonged effects of modified sham feeding on energy substrate mobilization.

BACKGROUND Vagal stimulation in response to nutrients is reported to elicit an array of digestive and endocrine responses, including an alteration in postprandial lipid metabolism. OBJECTIVE The objective of this study was to assess whether neural stimulation could alter hormone and substrate metabolism during the late postprandial phase, with implications for body fat mobilization. DESIGN Vagal stimulation was achieved by using the modified sham feeding (MSF) technique, in which nutrients are chewed and tasted but not swallowed. Ten healthy subjects were studied on 3 separate occasions, 4 wk apart. Five hours after a high-fat breakfast (56 g fat), the subjects were given 1 of 3 test meals allocated in random order: water, a lunch containing a modest amount of fat (38 g), or MSF (38 g fat). Blood was collected for 3 h poststimulus for hormone and metabolite analyses. RESULTS Plasma insulin and pancreatic polypeptide concentrations peaked at 250% and 209% of baseline concentrations within 15 min of MSF. The plasma glucose concentration increased significantly (P = 0.038) in parallel with the changes observed in the plasma insulin concentration. The nonesterified fatty acid concentration was significantly suppressed (P: = 0.006); maximum suppression occurred at a mean time of 114 min after MSF. This fall in nonesterified fatty acid was accompanied by a fall in the plasma glucagon concentration from 122 to 85 pmol/L (P = 0.018) at a mean time of 113 min after MSF. CONCLUSIONS Effects on substrate metabolism after MSF in the postprandial state differ from those usually reported in the postabsorptive state. The effects of MSF were prolonged beyond the period of the cephalic response and these may be relevant for longer-term metabolic regulation.
Severely dysregulated disposal of postprandial triacylglycerols exacerbates hypertriacylglycerolemia in HIV lipodystrophy syndrome.

BACKGROUND The pathogenesis of hypertriacylglycerolemia, a characteristic feature of HIV lipodystrophy syndrome (HLS), is incompletely understood. One mechanism is accelerated lipolysis in the fasted state, but the severity of the hypertriacylglycerolemia suggests that additional underlying abnormalities may exist in the disposal of dietary fat. OBJECTIVE Our objective was to investigate abnormalities in dietary fat disposal in the pathogenesis of hypertriacylglycerolemia in HLS. DESIGN We studied 6 nondiabetic men with HLS and 6 men without HIV matched for age and body mass index as control subjects for 8 h after consumption of an isocaloric meal containing 2 g labeled [(13)C(3)]tripalmitin. Chylomicron-triacylglycerol disposal was estimated from labeled [(13)C(1)]palmitate in the plasma chylomicron fraction, and [(13)C(1)]palmitate oxidation was estimated from the (13)CO(2) enrichment in the breath and CO(2) production, over 8 h after the meal. RESULTS HLS patients had significantly elevated concentrations of fasting plasma triacylglycerols in both chylomicron (x + SE: 100.3 +/- 49.5 compared with 29.2 +/- 2.2 mg/dL; P < 0.01) and VLDL (82.4 +/- 39.0 compared with 10.8 +/- 2.8 mg/dL; P < 0.01) fractions. Chylomicron-triacylglycerol-derived [(13)C(1)]palmitate disposal was markedly lower in the HLS patients (3.09 +/- 0.41 compared with 6.42 +/- 0.18 mmol [(13)C(1)]palmitate/8 h; P < 0.001) in the 8-h postmeal period. Further, HLS patients had lowered storage of chylomicron-triacylglycerols (0.74 +/- 0.38 compared with 5.05 +/- 0.16 mmol; P < 0.0001) and elevated plasma [(13)C(1)]palmitate concentrations (2.01 +/- 0.27 compared with 1.18 +/- 0.16 mmol; P < 0.05) 8 h after the meal. CONCLUSIONS Patients with HLS have key defects that markedly impair postprandial disposal and storage of chylomicron-triacylglycerols. These defects contribute significantly to hypertriacylglycerolemia in HLS.
Identification of nucleus pulposus precursor cells and notochordal remnants in the mouse: Implications for disk degeneration and chordoma formation

A classically identified “notochordal” cell population in the nucleus pulposus is thought to regulate disk homeostasis. However, the embryonic origin of these cells has been under dispute for >60 years. Here we provide the first direct evidence that all cell types in the adult mouse nucleus pulposus are derived from the embryonic notochord. Additionally, rare isolated embryonic notochord cells remained in the vertebral column and resembled “notochordal remnants,” which in humans have been proposed to give rise to a rare type of late‐onset cancer called chordoma. Previously, this cell type had not been identified in the mouse model system. The development and characterization of a mouse model that can be used to fate map nucleus pulposus precursor cells in any mutant background will be useful for uncovering the cellular and molecular mechanisms of disk degeneration. In addition, the identification of notochordal remnants in mice is the first step towards generating an in vivo model of chordoma. Developmental Dynamics 237:3953–3958, 2008. © 2008 Wiley‐Liss, Inc.
Transperitoneal laparoscopic pyeloplasty in children: does upper urinary tract anomalies affect surgical outcomes?

ABSTRACT Objective To assess the feasibility and outcomes of laparoscopic pyeloplasty in children with complex ureteropelvic junction obstruction (UPJO) and compare to children with iso-lated UPJO without associated urinary tract abnormalities. Material and Methods Medical records of 82 consecutive children submitted to transperi-toneal laparoscopic pyeloplasty in a 12-year period were reviewed. Eleven cases were con-sidered complex, consisting of atypical anatomy including horseshoe kidneys in 6 patients, pelvic kidneys in 3 patients, and a duplex collecting system in 2 patients. Patients were di-vided into 2 groups: normal anatomy (group 1) and complex cases (group 2). Demographics, perioperative data, outcomes and complications were recorded and analyzed. Results Mean age was 8.9 years (0.5-17.9) for group 1 and 5.9 years (0.5-17.2) for group 2, p=0.08. The median operative time was 200 minutes (180-230) for group 1 and 203 minutes (120-300) for group 2, p=0.15. Major complications (Clavien ≥3) were 4 (5.6%) in group 1 and 1 (6.3%) in group 2, p=0.52. No deaths or early postoperative complications such as: urinoma or urinary leakage or bleeding, occurred. The success rate for radiologic improvement and flank pain improvement was comparable between the two groups. Re-garding hydronephrosis, significant improvement was present in 62 patients (93.4%) of group 1 and 10 cases (90.9%) of group 2, p=0.99. The median hospital stay was 4 days (IQR 3-4) for group 1 and 4.8 days (IQR 3-6) for group 2, p=0.27. Conclusions Transperitoneal laparoscopic pyeloplasty is feasible and effective for the management of UPJO associated with renal or urinary tract anomalies.
A PI Consensus Controller for Networked Clocks Synchronization

Abstract In this paper we propose a novel distributed clock synchronization protocol for networks of clocks which have different initial offsets and internal clock speeds. The algorithm is based on an PI-like consensus protocol where the proportional (P) part compensates the different clock speeds while the integral part (I) eliminates the different clock offsets. This synchronization protocol is formally studied in its synchronous implementation and we provide both convergence guarantees as well optimal design using standard optimization tools when the underlaying communication graph is known. We also show how this protocol can be readily used to study the effect of noise and external disturbances on the steady-state performance. Finally, some simulations are presented.