Miracle-dz/UniFAR-FTUs huggingface dataset:
Fruit availability, chimpanzee diet, and grouping patterns on Rubondo Island, Tanzania

We examined seasonal patterns of fruit availability, dietary quality, and group size in the descendants of an introduced chimpanzee population on Rubondo Island, Tanzania. The site has supported a free‐ranging population without provisioning for 40 years. Our goals were to determine whether Rubondo chimpanzees experience periods of fruit shortage, and whether they respond to changes in fruit availability similarly to chimpanzees at endemic sites. We indexed the fruit availability of tree and liana species on transects stratified across three chimpanzee ranging areas. We used fecal analyses to evaluate seasonal changes in diet, and used data on party size and nesting group size to examine seasonal patterns of grouping. Tree fruit availability was positively correlated with rainfall, with a period of relative tree fruit scarcity corresponding with the long dry season. Liana fruit availability was not related to rainfall, and lianas exhibited less variable fruiting patterns across seasons. Fruits made up the majority of the chimpanzee diet, with lianas accounting for 35% of dietary fruit species. Fruits of the liana Saba comorensis were available during all months of phenological monitoring, but they were consumed more when tree fruit was scarce, suggesting that Saba comorensis fruits may be a fallback food for Rubondo chimpanzees. There were no increases in consumption of lower‐quality plant parts between seasons, and there were no changes in group size between seasons. These results contrast with evidence from several endemic chimpanzee study sites, and indicate that Rubondo chimpanzees may have access to abundant and high‐quality foods year round. Am. J. Primatol. 69:487–502, 2007. © 2007 Wiley‐Liss, Inc.
Efficient methods for encoding regions of interest in the upcoming JPEG2000 still image coding standard

The general method for generating the regions of interest (ROI) mask needed for encoding ROI in the upcoming JPEG2000 still image coding standard is presented. A simple method for the generation of the ROI mask for rectangular-shaped ROI is then proposed. Finally, to simplify the decoder when dealing with arbitrary shaped ROIs, a method for ROI coding that does not require any shape information to be transmitted to the decoder is described. A small coding penalty is associated with this method, while it makes it possible to have arbitrarily shaped ROI without the need of shape information and ROI mask generation at the decoder. The proposed methods have been included in the Final Committee Draft of JPEG2000 Part 1.
A Theory for Multiresolution Signal Decomposition: The Wavelet Representation

Multiresolution representations are effective for analyzing the information content of images. The properties of the operator which approximates a signal at a given resolution were studied. It is shown that the difference of information between the approximation of a signal at the resolutions 2/sup j+1/ and 2/sup j/ (where j is an integer) can be extracted by decomposing this signal on a wavelet orthonormal basis of L/sup 2/(R/sup n/), the vector space of measurable, square-integrable n-dimensional functions. In L/sup 2/(R), a wavelet orthonormal basis is a family of functions which is built by dilating and translating a unique function psi (x). This decomposition defines an orthogonal multiresolution representation called a wavelet representation. It is computed with a pyramidal algorithm based on convolutions with quadrature mirror filters. Wavelet representation lies between the spatial and Fourier domains. For images, the wavelet representation differentiates several spatial orientations. The application of this representation to data compression in image coding, texture discrimination and fractal analysis is discussed. >
The Importance of Hormesis to Public Health

Background Hormesis is a specific type of nonmonotonic dose response whose occurrence has been documented across a broad range of biological models, diverse types of exposure, and a variety of outcomes. The effects that occur at various points along this curve can be interpreted as beneficial or detrimental, depending on the biological or ecologic context in which they occur. Objective Because hormesis appears to be a relatively common phenomenon that has not yet been incorporated into regulatory practice, the objective of this commentary is to explore some of its more obvious public health and risk assessment implications, with particular reference to issues raised recently within this journal by other authors. Discussion Hormesis appears to be more common than dose–response curves that are currently used in the risk assessment process [e.g., linear no-threshold (LNT)]. Although a number of mechanisms have been identified that explain many hormetic dose–response relationships, better understanding of this phenomenon will likely lead to different strategies not only for the prevention and treatment of disease but also for the promotion of improved public health as it relates to both specific and more holistic health outcomes. Conclusions We believe that ignoring hormesis is poor policy because it ignores knowledge that could be used to improve public health.
Clinical Study Mortality in Levodopa-Treated Parkinson ’ s Disease

Parkinson's disease (PD) is associated with increased mortality despite many advances in treatment. Following the introduction of levodopa in the late 1960's, many studies reported improved or normalized mortality rates in PD. Despite the remarkable symptomatic benefits provided by levodopa, multiple recent studies have demonstrated that PD patients continue to die at a rate in excess of their peers. We undertook this retrospective study of 211 deceased PD patients to determine the factors associated with mortality in levodopa-treated PD. Our findings confirm that PD is associated with increased mortality in both men and women. Unlike the majority of other mortality studies, we found that women have a greater reduction in lifespan compared to men. We also found that patients with early onset PD (onset at the age of 50 or before) have reduced survival relative to PD patients with later ages of onset. A final important finding is that survival is equal in PD patients treated with levodopa early (within 2 years or less of PD onset) versus later.
Chaperone-like Activity of Tubulin*

Tubulin, a ubiquitous protein of eukaryotic cytoskeleton, is a building block unit of microtubule. Although several cellular processes are known to be mediated through the tubulin-microtubule system, the participation of tubulin or microtubule in protein folding pathway has not yet been reported. Here we show that goat brain tubulin has some functions and features similar to many known molecular chaperones. Substoichiometric amounts of tubulin can suppress the non-thermal and thermal aggregation of a number of unrelated proteins such as insulin, equine liver alcohol dehydrogenase, and soluble eye lens proteins containing β- and γ-crystallins. This chaperone-like activity of tubulin becomes more pronounced as temperature increases. Aging of tubulin solution at 37 °C also enhances its chaperone-like activity. Tubulin loses its chaperone-like activity upon removal of its flexible hydrophilic C-terminal tail. These results suggest that both electrostatic and hydrophobic interactions are important in substrate binding by tubulin and that the negatively charged C-terminal tails play a crucial role for its chaperone-like activity.
Second primary cancers after cancer of unknown primary in Sweden and Germany: efficacy of the modern work-up

In unsparing efforts to find the hidden primaries, second primary cancers (SPCs) unrelated to cancer of unknown primary (CUP) are found. The detection rates of SPCs after CUP can be considered as measures for the effectiveness of modern diagnostic techniques in finding tumors. We aimed to compare the rates of specific SPCs found after the work-up of CUP and the more sign/symptom-directed diagnostic approaches applied after any other cancer. The number of CUP patients identified in the nationwide Swedish database and nine German cancer registries was 24 641 from 1997 through 2006, and rate ratios (RRs) for SPCs were recorded in two follow-up periods. The detection rate of SPCs immediately after any other cancer was about two times higher in Germany than in Sweden, but the rate immediately after CUP was almost the same for the two datasets. In the joint analyses after CUP, the RRs of liver, lung, breast, and kidney cancers were higher than after any other cancer, whereas the RRs of prostate, urinary bladder, and connective tissue cancers as well as non-Hodgkin’s lymphoma were not significantly different; the RR of cancers of upper aerodigestive tract was lower after CUP than after any other cancer. The joint data indicate that the work-up is efficient in detecting tumors in the thoracoabdominal organs that are screened by computed tomography. For some other organ sites, the more sign/symptom-directed diagnostic approaches may be equally efficient. However, none of the applied techniques could detect all tumors immediately after the first diagnosis.
Exploiting the Classification Performance of Support Vector Machines with Multi-Temporal Moderate-Resolution Imaging Spectroradiometer (MODIS) Data in Areas of Agreement and Disagreement of Existing Land Cover Products

Several studies have focused in the past on global land cover (LC) datasets harmonization and inter-comparison and have found significant inconsistencies. Despite the known discrepancies between existing products derived from medium resolution satellite sensor data, little emphasis has been placed on examining these disagreements to improve the overall classification accuracy of future land cover maps. This work evaluates the classification performance of a least square support vector machine (LS-SVM) algorithm with respect to areas of agreement and disagreement between two existing land cover maps. The approach involves the use of time series of Moderate-resolution Imaging Spectroradiometer (MODIS) 250-m Normalized Difference Vegetation Index (NDVI) (16-day composites) and gridded climatic indicators. LS-SVM is trained on reference samples obtained through visual interpretation of Google Earth (GE) high resolution imagery. The core of the training process is based on repeated random splits of the training dataset to select a small set of suitable support vectors optimizing class separability. A large number of independent validation samples spread over three contrasting regions in Europe (Eastern Austria, Macedonia and Southern France) are used to calculate classification accuracies for the LS-SVM NDVI-derived LC map and for two (globally available) LC products: GLC2000 and GlobCover. The LS-SVM LC map reported an overall accuracy of 70%. Classification accuracies ranged from 71% where GlobCover and GLC2000 agreed to 68% for areas of disagreement. Results indicate that existing LC products are as accurate as the LS-SVM LC map in areas of agreement (with little margin for improvements), while classification accuracy is substantially better for the LS-SVM LC map in areas of disagreement. On average, the LS-SVM LC map was 14% and 18% more accurate compared to GlobCover and GLC2000, respectively.
Identification of a ternary protein-complex as a therapeutic target for K-Ras-dependent colon cancer

A cancer phenotype is driven by several proteins and targeting a cluster of functionally interdependent molecules should be more effective for therapeutic intervention. This is specifically important for Ras-dependent cancer, as mutated (MT) Ras is non-druggable and targeting its interaction with effectors may be essential for therapeutic intervention. Here, we report that a protein-complex activated by the Ras effector p38γ MAPK is a novel therapeutic target for K-Ras-dependent colon cancer. Unbiased proteomic screening and immune-precipitation analyses identified p38γ interaction with heat shock protein 90 (Hsp90) and K-Ras in K-Ras MT, but not wild-type (WT), colon cancer cells, indicating a role of this complex in Ras-dependent growth. Further experiments showed that this complex requires p38γ and Hsp90 activity to maintain MT, but not WT, K-Ras protein expression. Additional studies demonstrated that this complex is activated by p38γ-induced Hsp90 phosphorylation at S595, which is important for MT K-Ras stability and for K-Ras dependent growth. Of most important, pharmacologically inhibition of Hsp90 or p38γ activity disrupts the complex, decreases K-Ras expression, and selectively inhibits the growth of K-Ras MT colon cancer in vitro and in vivo. These results demonstrated that the p38γ-activated ternary complex is a novel therapeutic target for K-Ras-dependent colon cancer.
18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry*

Selected reaction monitoring (SRM)-MS is an emerging technology for high throughput targeted protein quantification and verification in biomarker discovery studies; however, the cost associated with the application of stable isotope-labeled synthetic peptides as internal standards can be prohibitive for screening a large number of candidate proteins as often required in the preverification phase of discovery studies. Herein we present a proof of concept study using an 18O-labeled proteome reference as global internal standards (GIS) for SRM-based relative quantification. The 18O-labeled proteome reference (or GIS) can be readily prepared and contains a heavy isotope (18O)-labeled internal standard for every possible tryptic peptide. Our results showed that the percentage of heavy isotope (18O) incorporation applying an improved protocol was >99.5% for most peptides investigated. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into the labeled mouse plasma reference. Reliable quantification was observed with high reproducibility (i.e. coefficient of variance <10%) for analyte concentrations that were set at 100-fold higher or lower than those of the GIS based on the light (16O)/heavy (18O) peak area ratios. The utility of 18O-labeled GIS was further illustrated by accurate relative quantification of 45 major human plasma proteins. Moreover, quantification of the concentrations of C-reactive protein and prostate-specific antigen was illustrated by coupling the GIS with standard additions of purified protein standards. Collectively, our results demonstrated that the use of 18O-labeled proteome reference as GIS provides a convenient, low cost, and effective strategy for relative quantification of a large number of candidate proteins in biological or clinical samples using SRM.
Design and Implementation of Performance Metrics for Evaluation of Assessments Data

The objective of this paper is to design performance metrics and respective formulas to quantitatively evaluate the achievement of set objectives and expected outcomes both at the course and program levels. Evaluation is defined as one or more processes for interpreting the data acquired through the assessment processes in order to determine how well the set objectives and outcomes are being attained. Even though assessment processes for accreditation are well documented but existence of an evaluation process is assumed. This paper focuses on evaluation process to provide insights and techniques for data interpretation. It gives a complete evaluation process from the data collection through various assessment methods, performance metrics, to the presentations in the form of tables and graphs. Authors hope that the articulated description of evaluation formulas will help convergence to high quality standard in evaluation process.
A century of variation in the dependence of Greenland iceberg calving on ice sheet surface mass balance and regional climate change

Iceberg calving is a major component of the total mass balance of the Greenland ice sheet (GrIS). A century-long record of Greenland icebergs comes from the International Ice Patrol's record of icebergs (I48N) passing latitude 48° N, off Newfoundland. I48N exhibits strong interannual variability, with a significant increase in amplitude over recent decades. In this study, we show, through a combination of nonlinear system identification and coupled ocean–iceberg modelling, that I48N's variability is predominantly caused by fluctuation in GrIS calving discharge rather than open ocean iceberg melting. We also demonstrate that the episodic variation in iceberg discharge is strongly linked to a nonlinear combination of recent changes in the surface mass balance (SMB) of the GrIS and regional atmospheric and oceanic climate variability, on the scale of the previous 1–3 years, with the dominant causal mechanism shifting between glaciological (SMB) and climatic (ocean temperature) over time. We suggest that this is a change in whether glacial run-off or under-ice melting is dominant, respectively. We also suggest that GrIS calving discharge is episodic on at least a regional scale and has recently been increasing significantly, largely as a result of west Greenland sources.
Taurodontism, variations in tooth number, and misshapened crowns in Wnt10a null mice and human kindreds

WNT10A is a signaling molecule involved in tooth development, and WNT10A defects are associated with tooth agenesis. We characterized Wnt10a null mice generated by the knockout mouse project (KOMP) and six families with WNT10A mutations, including a novel p.Arg104Cys defect, in the absence of EDA, EDAR, or EDARADD variations. Wnt10a null mice exhibited supernumerary mandibular fourth molars, and smaller molars with abnormal cusp patterning and root taurodontism. Wnt10a−/− incisors showed distinctive apical–lingual wedge‐shaped defects. These findings spurred us to closely examine the dental phenotypes of our WNT10A families. WNT10A heterozygotes exhibited molar root taurodontism and mild tooth agenesis (with incomplete penetrance) in their permanent dentitions. Individuals with two defective WNT10A alleles showed severe tooth agenesis and had fewer cusps on their molars. The misshapened molar crowns and roots were consistent with the Wnt10a null phenotype and were not previously associated with WNT10A defects. The missing teeth contrasted with the presence of supplemental teeth in the Wnt10a null mice and demonstrated mammalian species differences in the roles of Wnt signaling in early tooth development. We conclude that molar crown and root dysmorphologies are caused by WNT10A defects and that the severity of the tooth agenesis correlates with the number of defective WNT10A alleles.
Reliability of the NINDS common data elements cranial tomography (CT) rating variables for traumatic brain injury (TBI)

ABSTRACT Background: Non-contrast head computer tomography (CT) is widely used to evaluate eligibility of patients after acute traumatic brain injury (TBI) for clinical trials. The NINDS Common Data Elements (CDEs) TBI were developed to standardize collection of CT variables. The objectives of this study were to train research assistants (RAs) to rate CDEs and then to evaluate their performance. The aim was to assess inter-rater reliability (IRR) of CDEs between trained RAs and a neurologist and to evaluate applicability of CDEs in acute and sub-acute TBI to test the feasibility of using CDE CT ratings in future trials and ultimately in clinical practice. The second aim was to confirm that the ratings of CDEs reflect pathophysiological events after TBI. Methods and results: First, a manual was developed for application of the CDEs, which was used to rate brain CTs (n = 100). An excellent agreement was found in combined kappas between RAs on admission and on 24-hour follow-up CTs (Iota = 0.803 and 0.787, respectively). Good IRR (kappa > 0.61) was shown for six CDEs on admissions and for seven CDEs on follow-up CTs. Low IRR (kappa < 0.4) was determined for five CDEs on admission and for four CDEs on follow-up CT. Combined IRR of each assistant with the neurologist were good on admission (Iota = 0.613 and 0.787) and excellent on follow-up CT (Iota = 0.906 and 0.977). Second, Principal Component Analysis (PCA) was applied to cluster the rated CDEs (n = 255) and five major components were found that explain 53% of the variance. Conclusions: CT CDEs are useful in clinical studies of TBI. Trained RAs can reliably collect variables. PCA identifies CDE clusters with clinical and biologic plausibility. Abbreviations: RA, research assistant; CT, Cranial Tomography; TBI, Traumatic Brain Injury; CDE, Common Data Elements; IRR, inter-rater reliability; PCA, Principal Component Analysis; GCS, Glasgow Coma Scale; R, rater; CI, confidence interval; CCC, Concordance correlation coefficient; IVH, Intraventricular haemorrhage; DCA, Discriminant Component analysis; SAH, Subarachnoid Haemorrhage
Sexual segregation of pelagic sharks and the potential threat from fisheries

Large pelagic sharks are declining in abundance in many oceans owing to fisheries exploitation. What is not known however is whether within-species geographical segregation of the sexes exacerbates this as a consequence of differential exploitation by spatially focused fisheries. Here we show striking sexual segregation in the fastest swimming shark, the shortfin mako Isurus oxyrinchus, across the South Pacific Ocean. The novel finding of a sexual ‘line in the sea’ spans a historical longline-fishing intensity gradient, suggesting that differential exploitation of the sexes is possible, a phenomenon which may underlie changes in the shark populations observed elsewhere.
PML risk stratification using anti-JCV antibody index and L-selectin

Background: Natalizumab treatment is associated with progressive multifocal leukoencephalopathy (PML) development. Treatment duration, prior immunosuppressant use, and JCV serostatus are currently used for risk stratification, but PML incidence stays high. Anti-JCV antibody index and L-selectin (CD62L) have been proposed as additional risk stratification parameters. Objective: This study aimed at verifying and integrating both parameters into one algorithm for risk stratification. Methods: Multicentric, international cohorts of natalizumab-treated MS patients were assessed for JCV index (1921 control patients and nine pre-PML patients) and CD62L (1410 control patients and 17 pre-PML patients). Results: CD62L values correlate with JCV serostatus, as well as JCV index values. Low CD62L in natalizumab-treated patients was confirmed and validated as a biomarker for PML risk with the risk factor “CD62L low” increasing a patient’s relative risk 55-fold (p < 0.0001). Validation efforts established 86% sensitivity/91% specificity for CD62L and 100% sensitivity/59% specificity for JCV index as predictors of PML. Using both parameters identified 1.9% of natalizumab-treated patients in the reference center as the risk group. Conclusions: Both JCV index and CD62L have merit for risk stratification and share a potential biological relationship with implications for general PML etiology. A risk algorithm incorporating both biomarkers could strongly reduce PML incidence.
Optimal control of a wave energy converter

The optimal control strategy for a wave energy converter (WEC) with constraints on the control torque is investigated. The goal is to optimize the total energy delivered to the electricity grid. Using Pontryagin's maximum principle, the solution is found to be singular-bang. Using higher order conditions, the optimal control on the singular arc is found as a function of the state and costate trajectories. Furthermore, it is shown that the transitions between bang and singular subarcs are discontinuous. Based on these findings the results of a numerical direct method are validated. Finally, the optimal control is used to benchmark an existing MPC strategy. It is found that for active control torque constraints the MPC strategy does not result in the discontinuous singular-bang transitions. However, the difference in harvested power is small.