Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood mRNA Measurement (NETest) for Neuroendocrine Tumor Diagnosis of Image-Negative Liver Metastatic Disease

Context Early cancer detection is critical to optimize treatment. This is particularly problematic in neuroendocrine tumors (NETs), which exhibit an ∼5-year diagnostic delay due to covert symptoms, limitations in imaging, and circulating biomarkers. Despite development of continuous monitoring strategies utilizing advanced modalities [CT/MRI or 68Gallium positron emission tomography (PET)/CT] or a repertoire of monoanalyte biomarkers [e.g., chromogranin A (CgA), pancreastatin, serotonin], detection of minimal residual disease or microrecurrence remains elusive. Emerging molecular liquid biopsies (e.g., NETest) provide a substantially improved threshold for disease detection. Case Description We describe the utility of a blood-based multigene PCR neuroendocrine measurement (NETest), which is representative of core molecular drivers of neuroendocrine tumorigenesis, to detect hepatic micrometastases in a patient with negative blood biomarkers and negative anatomical/functional imaging. The 52-year-old woman, who had undergone margin-negative resection for a NET of the ileocecal valve, developed persistently elevated NETest levels 8 months later. CT/MRI/68Gallium PET and biomarkers remained negative. Blood multigene analysis identified disease, and peptide receptor radionuclide therapy (PRRT) was undertaken. Over 9 months, NETest levels increased (conventional biomarkers/imaging remained normal). Liver biopsy was undertaken, and foci of a 3-mm NET in segment VI were histologically documented. At 3.3 years after PRRT, the disease remained as a microscopic burden and stable biomarker/68Gallium PET/MRI occult despite elevated blood levels of NET genes. Conclusions Blood measurement of NET transcripts can identify image- and CgA-negative disease. A NET liquid biopsy strategy has clinical utility in the early identification of residual or metastatic disease and optimizes consideration of adjuvant therapeutic intervention.
Established and emerging strategies to crack the genetic code of obesity

Tremendous progress has been made in the genetic elucidation of obesity over the past two decades, driven largely by technological, methodological and organizational innovations. Current strategies for identifying obesity‐predisposing loci/genes, including cytogenetics, linkage analysis, homozygosity mapping, admixture mapping, candidate gene studies, genome‐wide association studies, custom genotyping arrays, whole‐exome sequencing and targeted exome sequencing, have achieved differing levels of success, and the identified loci in aggregate explain only a modest fraction of the estimated heritability of obesity. This review outlines the successes and limitations of these approaches and proposes novel strategies, including the use of exceptionally large sample sizes, the study of diverse ethnic groups and deep phenotypes and the application of innovative methods and study designs, to identify the remaining obesity‐predisposing genes. The use of both established and emerging strategies has the potential to crack the genetic code of obesity in the not‐too‐distant future. The resulting knowledge is likely to yield improvements in obesity prediction, prevention and care.
A Novel Fundus Image Reading Tool for Efficient Generation of a Multi-dimensional Categorical Image Database for Machine Learning Algorithm Training

Background We described a novel multi-step retinal fundus image reading system for providing high-quality large data for machine learning algorithms, and assessed the grader variability in the large-scale dataset generated with this system. Methods A 5-step retinal fundus image reading tool was developed that rates image quality, presence of abnormality, findings with location information, diagnoses, and clinical significance. Each image was evaluated by 3 different graders. Agreements among graders for each decision were evaluated. Results The 234,242 readings of 79,458 images were collected from 55 licensed ophthalmologists during 6 months. The 34,364 images were graded as abnormal by at-least one rater. Of these, all three raters agreed in 46.6% in abnormality, while 69.9% of the images were rated as abnormal by two or more raters. Agreement rate of at-least two raters on a certain finding was 26.7%–65.2%, and complete agreement rate of all-three raters was 5.7%–43.3%. As for diagnoses, agreement of at-least two raters was 35.6%–65.6%, and complete agreement rate was 11.0%–40.0%. Agreement of findings and diagnoses were higher when restricted to images with prior complete agreement on abnormality. Retinal/glaucoma specialists showed higher agreements on findings and diagnoses of their corresponding subspecialties. Conclusion This novel reading tool for retinal fundus images generated a large-scale dataset with high level of information, which can be utilized in future development of machine learning-based algorithms for automated identification of abnormal conditions and clinical decision supporting system. These results emphasize the importance of addressing grader variability in algorithm developments.
Pigmentation and not only sex and age of individuals affects despotism in the Andean condor

Attributes such as sex, age and pigmentation of individuals could correspond to the competitive skills they use to access resources and, consequently, determine their social status when a hierarchy of dominance is established. We analysed patterns of social dominance in relation to sex, age and, for the first time, according to face pigmentation in a large scavenger bird species, the Andean condor (Vultur gryphus). This species displays extreme sexual dimorphism, with males being up to 50% heavier than females. Associated to this, strong hierarchical relationships characterize foraging, roosting and breeding. We recorded agonistic interactions within condor groups while foraging through video recordings in experimental stations. We corroborated a strong despotism by the adult males to the rest of the categories. More interestingly we found this despotism was also expressed by most pigmented birds; juvenile females being completely subordinated and, at the same time, not expressing pigmentation. Importantly, when condors of equal sex and age category fought, the more pigmented individuals were successful. Our results highlight that pigmentation, besides sex and age, is an attribute that also corresponds with social status in the Andean condor, making its hierarchical system more complex.
Perceptions of occupational therapy students and clinical tutors on the attributes of a good role model

Abstract Background: Occupational therapy students learn in different environments, where role modelling takes place. Nevertheless, little is known about student and tutors perceptions on model´s characteristics. Objectives: The aims of this study were to investigate the perceptions of occupational therapy students on the most important attributes of role models and to confront their views with those of clinical tutors. Methods: A sample of 61 students completed a structured, standardized online questionnaire. Ten clinical tutors regarded by students as good models underwent a semi-structured individual interview. Data were analyzed quantitatively and qualitatively (thematic content analysis). Results: The most important attributes of a good role model according to student perception were: good relationship with patients, integrity and ethical behaviour, respectful relationships with colleagues, patient management skills, commitment to personal and professional growth and enthusiasm for the profession. Clinical tutors believed that they were nominated as good role models because they demonstrated empathy towards patients, good relationships with students and enthusiasm for their profession. Conclusions and Significance: Perceptions of occupational therapy students and clinical tutors about role models characteristics were similar. Identification of attributes of good role models may inform teacher training and faculty development in occupational therapy.
Scavenging of lipid peroxyl radicals protects plasma lipids and proteins from peroxynitrite

Peroxynitrite can be produced in the vasculature from a superoxide anion reaction with nitric oxide. A surplus of peroxynitrite in the intravascular compartment is a common feature of several chronic diseases. The development of pharmacological modalities that interfere with the formation of peroxynitrite or inhibit its oxidative damage may be of utility for the prevention and/or treatment of several pathologies. Our previous investigations showed that catalytically inactivating peroxynitrite-derived free radicals with tempol or scavenging reactive aldehyde species with phenelzine protects the blood plasma and platelets from the oxidative damage of peroxynitrite. However, the degree of inhibition of the cytotoxic effects of peroxynitrite using tempol or phenelzine was modest. In the present study, the aim was to examine if scavenging lipid peroxyl radicals with U-83836E can achieve superior protection from peroxynitrite. This was assessed by treating blood plasma or platelets with 100 µM peroxynitrite alone or in combination with U-83836E, and then measuring the levels of thiobarbituric acid reactive substances (TBARS) and protein carbonyl formation as indices of lipid peroxidation and protein oxidation, respectively. It was observed that scavenging lipid peroxyl radicals with 75-100 µM U-83836E increasingly reversed protein carbonylation induced by peroxynitrite in blood plasma and platelets, in addition to TBARS formation in blood plasma. These findings are further discussed in the context of the mechanisms by which U-83836E may protect against the cell-damaging effects of peroxynitrite.
Relative skeletal distribution of proliferating marrow in the adult dog determined using 3′‐deoxy‐3′‐[18F]fluorothymidine

3′‐deoxy‐3′‐[18F]fluorothymidine (18FLT) is a radiopharmaceutical tracer used with positron emission tomography (PET), often in combination with computed tomography (CT), to image DNA synthesis, and thus, cellular proliferation. Characteristic accumulation of the tracer within haematopoietic bone marrow provides a noninvasive means to assess marrow activity and distribution throughout the living animal. The present study utilizes three‐dimensional analysis of 18FLT‐PET/CT scans to quantify the relative skeletal distribution of active marrow by anatomic site in the dog. Scans were performed on six healthy, adult (3–6 years of age), mixed‐breed dogs using a commercially available PET/CT scanner consisting of a 64‐slice helical CT scanner combined with an integrated four ring, high‐resolution LSO PET scanner. Regions of interest encompassing 11 separate skeletal regions (skull, cervical vertebral column, thoracic vertebral column, lumbar vertebral column, sacrum, ribs, sternum, scapulae, proximal humeri, ossa coxarum, and proximal femora) were manually drawn based on CT images and thresholded by standardized uptake value to delineate bone marrow activity. Activity within each skeletal region was then divided by the total skeletal activity to derive the per cent of overall marrow activity within an individual site. The majority of proliferative marrow was located within the vertebral column. Of the sites traditionally accessed clinically for marrow sampling, the proximal humerus contained the largest percentage, followed by the ossa coxarum, proximal femur, and sternum, respectively. This information may be used to guide selection of traditional marrow sampling sites as well as inform efforts to spare important sites of haematopoiesis in radiation therapy planning.
Comparison and Noise Suppression of the Transmitted and Reflected Photoplethysmography Signals

The photoplethysmography (PPG) is inevitably corrupted by many kinds of noise no matter whether its acquisition mode is transmittance or reflectance. To enhance the quality of PPG signals, many studies have made great progress in PPG denoising by adding extra sensors and developing complex algorithms. Considering the reasonable cost, compact size, and real-time and easy implementation, this study proposed a simple real-time denoising method based on double median filters which can be integrated in microcontroller of commercial or portable pulse oximeters without adding extra hardware. First, we used the boundary extension to preserve the signal boundary distortion and designed a first median filter with the time window at approximately 78 ms to eliminate the high-frequency components of the signal. Then, through the second median filter with a time window which was about 780 ms, we estimated the low-frequency components. Finally, we removed the estimated low-frequency components from the signal to obtain the denoised signal. Through comparing the multiple sets of signals under calmly sitting and slightly moving postures, the PPG signals contained noises no matter whether collected by the transmittance-mode or the reflectance-mode. To evaluate the proposed method, we conducted measured, simulated experiments and a strong noisy environment experiment. Through comparing the morphology distortions, frequency spectra, and the signal-to-noise ratios (SNRs), the results showed that the proposed method can suppress noise effectively and preserve the essential morphological features from PPG signals. As a result, the proposed method can enhance the quality of PPG signals and, thus, can contribute to the improvement of the calculation accuracy of the subsequent physiological parameters. In addition, the proposed method could be a good choice to address the real-time noise reduction of portable PPG measuring instruments.
Breathe Easy, Speak Easy: Pulmonary Function and Language Performance in Aging

ABSTRACT Background: This study explored the association between pulmonary function (PF) and older adults’ language performance accuracy. Study rationale was anchored in aging research reporting PF as a reliable risk factor affecting cognition among the elderly. Methods: 180 adult English native speakers aged 55 to 84 years participated in the study. PF was measured through forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio (FFR). Language performance was assessed with an action naming test and an object naming test, and two tests of sentence comprehension, one manipulating syntactic complexity and the other, semantic negation. Greater PF was predicted to be positively associated with all tasks. Results: Unadjusted models revealed FVC and FEV1 effects on language performance among older adults. Participants with higher FVC showed better naming on both tasks and those with higher FEV1 had better object naming only. In covariate-adjusted models, only a positive FVC-object naming association remained. Conclusion: Findings were discussed in terms of brain oxygenation mechanisms, whereby good PF may implicate efficient oxygenation, supporting neurotransmitter metabolism that protects against neural effects of cerebrovascular risk. Effects on object naming were linked to putative differential oxygenation demands across language tasks.
Emergent mechanisms of evidence integration in recurrent neural networks

Recent advances in machine learning have enabled neural networks to solve tasks humans typically perform. These networks offer an exciting new tool for neuroscience that can give us insight in the emergence of neural and behavioral mechanisms. A big gap remains though between the very deep neural networks that have risen in popularity and outperformed many existing shallow networks in the field of computer vision and the highly recurrently connected human brain. This trend towards ever-deeper architectures raises the question why the brain has not developed such an architecture. Besides wiring constraints we argue that the brain operates under different circumstances when performing object recognition, being confronted with noisy and ambiguous sensory input. The role of time in the process of object recognition is investigated, showing that a recurrent network trained through reinforcement learning is able to learn the amount of time needed to arrive at an accurate estimate of the stimulus and develops behavioral and neural mechanisms similar to those found in the human and non-human primate literature.
Birth seasons and heights among girls and boys below 12 years of age: lasting effects and catch-up growth among native Amazonians in Bolivia

Abstract Background: Seasons affect many social, economic, and biological outcomes, particularly in low-resource settings, and some studies suggest that birth season affects child growth. Aim: To study a predictor of stunting that has received limited attention: birth season. Subjects and methods: This study uses cross-sectional data collected during 2008 in a low-resource society of horticulturists-foragers in the Bolivian Amazon, Tsimane’. It estimates the associations between birth months and height-for-age Z-scores (HAZ) for 562 girls and 546 boys separately, from birth until age 11 years or pre-puberty, which in this society occurs ∼13–14 years. Results: Children born during the rainy season (February–May) were shorter, while children born during the end of the dry season and the start of the rainy season (August–November) were taller, both compared with their age–sex peers born during the rest of the year. The correlations of birth season with HAZ were stronger for boys than for girls. Controlling for birth season, there is some evidence of eventual partial catch-up growth, with the HAZ of girls or boys worsening until ∼ age 4–5 years, but improving thereafter. By age 6 years, many girls and boys had ceased to be stunted, irrespective of birth season. Conclusion: The results suggest that redressing stunting will require attention to conditions in utero, infancy and late childhood.
ATP compartmentation in plastids and cytosol of Arabidopsis thaliana revealed by fluorescent protein sensing

Significance By studying in vivo changes of ATP levels in the plastids and cytosol of Arabidopsis thaliana using a FRET-based ATP sensor, we show that the plastidic ATP concentrations in cotyledon, hypocotyl, and root of 10-day-old seedlings are significantly lower than the cytosolic concentrations. We show that chloroplasts consume ATP rapidly and the import of ATP into mature chloroplasts is impeded by the low density of NTT transporter. Hence, unlike in diatoms, where ATP is imported into chloroplasts to support the Calvin–Benson–Bassham (CBB) cycle, mature chloroplasts of Arabidopsis do not balance the ATP:NADPH ratio by importing ATP from the cytosol. Rather, chloroplasts can export surplus reducing equivalents, which can be used by the mitochondria to supply ATP to the cytosol. Matching ATP:NADPH provision and consumption in the chloroplast is a prerequisite for efficient photosynthesis. In terms of ATP:NADPH ratio, the amount of ATP generated from the linear electron flow does not meet the demand of the Calvin–Benson–Bassham (CBB) cycle. Several different mechanisms to increase ATP availability have evolved, including cyclic electron flow in higher plants and the direct import of mitochondrial-derived ATP in diatoms. By imaging a fluorescent ATP sensor protein expressed in living Arabidopsis thaliana seedlings, we found that MgATP2− concentrations were lower in the stroma of mature chloroplasts than in the cytosol, and exogenous ATP was able to enter chloroplasts isolated from 4- and 5-day-old seedlings, but not chloroplasts isolated from 10- or 20-day-old photosynthetic tissues. This observation is in line with the previous finding that the expression of chloroplast nucleotide transporters (NTTs) in Arabidopsis mesophyll is limited to very young seedlings. Employing a combination of photosynthetic and respiratory inhibitors with compartment-specific imaging of ATP, we corroborate the dependency of stromal ATP production on mitochondrial dissipation of photosynthetic reductant. Our data suggest that, during illumination, the provision and consumption of ATP:NADPH in chloroplasts can be balanced by exporting excess reductants rather than importing ATP from the cytosol.
Multi-Target Track-to-Track Fusion Based on Permutation Matrix Track Association

This paper proposes the Permutation Matrix Track Association (PMTA) algorithm to support track-to-track, multi-sensor data fusion for multiple targets in an autonomous driving system. In this system, measurement data from different sensor modalities (LIDAR, radar, and vision) is processed by object trackers operating on each sensor modality independently to create the tracks of the objects. The proposed approach fuses the object track lists from each tracker, first by associating the tracks within each track list, followed by a state estimation (filtering) step. The eventual output is the unified tracks of the objects provided for further autonomous driving processing, such as path and motion planning. The permutation matrix track association (PMTA) algorithm considers both spatial and temporal information to associate object tracks from different sensor modalities. Experimental results show that the proposed approach improves not only the performance of the multipletarget track-to-track fusion, but also stability and robustness in the resulting speed control and decision making in the autonomous driving system.
Exactly Solving the Maximum Weight Independent Set Problem on Large Real-World Graphs

One powerful technique to solve NP-hard optimization problems in practice is branch-and-reduce search---which is branch-and-bound that intermixes branching with reductions to decrease the input size. While this technique is known to be very effective in practice for unweighted problems, very little is known for weighted problems, in part due to a lack of known effective reductions. In this work, we develop a full suite of new reductions for the maximum weight independent set problem and provide extensive experiments to show their effectiveness in practice on real-world graphs of up to millions of vertices and edges. Our experiments indicate that our approach is able to outperform existing state-of-the-art algorithms, solving many instances that were previously infeasible. In particular, we show that branch-and-reduce is able to solve a large number of instances up to two orders of magnitude faster than existing (inexact) local search algorithms---and is able to solve the majority of instances within 15 minutes. For those instances remaining infeasible, we show that combining kernelization with local search produces higher-quality solutions than local search alone.
Where Are the Dads? A Pilot Study of a Dads-Only Session in Group Prenatal Care

Despite suggestions that paternal engagement is one potential strategy to impact the multifaceted problem of infant mortality, fathers' involvement in prenatal care has received little attention or study. While there is evidence that fathers want information about assisting partners and caring for newborns, the best mechanism for providing this information is unknown. A pilot study was conducted using a father-only session designed to provide information in an informal, interactive setting within a model of group prenatal care. All 5 of the fathers approached agreed to participate. The fathers participating in this session indicated that the session was beneficial and found it to be a valuable addition to the group care model. Implications for health providers include identifying opportunities that allow fathers to share concerns and anxieties regarding care for partners and newborns. Implementing fathering activities into group prenatal care or developing other opportunities for fathers to be involved prenatally needs further investigation.