Miracle-dz/UniFAR-FTUs huggingface dataset:
Can Text Messages Reach the Parts Other Process Measures Cannot Reach: An Evaluation of a Behavior Change Intervention Delivered by Mobile Phone?

Background Process evaluation is essential in developing, piloting and evaluating complex interventions. This often involves observation of intervention delivery and interviews with study participants. Mobile telephone interventions involve no face to face contact, making conventional process evaluation difficult. This study assesses the utility of novel techniques for process evaluation involving no face to face contact. Methods Text messages were delivered to 34 disadvantaged men as part of a feasibility study of a brief alcohol intervention. Process evaluation focused on delivery of the text messages and responses received from study participants. The computerized delivery system captured data on receipt of the messages. The text messages, delivered over 28 days, included nine which asked questions. Responses to these questions served as one technique for process evaluation by ascertaining the nature of engagement with the study and with steps on the causal chain to behavior change. Results A total of 646 SMS text messages were sent to participants. Of these, 613 messages (95%) were recorded as delivered to participants’ telephones. 88% of participants responded to messages that asked questions. There was little attenuation in responses to the questions across the intervention period. Content analysis of the responses revealed that participants engaged with text messages, thought deeply about their content and provided carefully considered personal responses to the questions. Conclusions Socially disadvantaged men, a hard to reach population, engaged in a meaningful way over a sustained period with an interactive intervention delivered by text message. The novel process measures used in the study are unobtrusive, low cost and collect real-time data on all participants. They assessed the fidelity of delivery of the intervention and monitored retention in the study. They measured levels of engagement and identified participants’ reactions to components of the intervention. These methods provide a valuable addition to conventional process evaluation techniques.
Approximate manipulability of leader-follower networks

We introduce the notion of manipulability to leader-follower networks as a tool to analyze how effective inputs injected at a leader node are in terms of their impact on the movements of the follower nodes, as a function of the interaction topologies and agent configurations. Classic manipulability is an index used in robotics for analyzing the singularity and efficiency of configurations of robot-arm manipulators. To define similar notions for leader-follower networks, we use a rigid-link approximation of the follower dynamics and under this assumption, we prove that the instantaneous follower velocities can be uniquely determined by that of the leader's, which allows us to define a meaningful manipulability index of the leader-follower networks.
Utilization of physician services for diabetic patients from ethnic minorities.

BACKGROUND Diabetes is a common chronic disease, which results in significant morbidity and mortality. Although ethnic variations in disease prevalence are known, variations in the utilization of physician services for the disease (particularly in publicly funded health care systems) are uncertain. METHODS Self-reported ethnicity was determined from two population health surveys in Ontario, Canada. These data were linked to administrative data sources, including an administrative data-derived disease registry. Diabetes prevalence was determined for each ethnic group. Utilization of physician services for primary care, diabetes specialist care and eye examinations was compared among ethnic groups, adjusting for age, sex, socioeconomic status and diabetes duration. RESULTS There were 20,788 eligible survey respondents. Standardized diabetes prevalence was elevated for the South Asian and Black populations (11.1 and 11.0%, respectively) compared with that for the White population (5.9%). Ethnic minorities with diabetes were less likely to receive an eye examination compared with White patients (adjusted OR, 0.63; 95% CI, 0.46-0.85). The use of primary care and diabetes specialist care did not differ. CONCLUSION Ethnic minorities with diabetes are less likely to receive eye examinations. This disparity in quality of care could lead to worse clinical outcomes for these patients.
Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming

In this paper, we study control problems of Boolean Networks (BNs) and Probabilistic Boolean Networks (PBNs). For BN CONTROL, by applying external control, we propose to derive the network to the desired state within a few time steps. For PBN CONTROL, we propose to find a control sequence such that the network will terminate in the desired state with a maximum probability. Also, we propose to minimize the maximum cost of the terminal state to which the network will enter. Integer linear programming and dynamic programming in conjunction with hard constraints are then employed to solve the above problems. Numerical experiments are given to demonstrate the effectiveness of our algorithms. We also present a hardness result suggesting that PBN CONTROL is harder than BN CONTROL.
A new index to optimally design and compare continuous glucose monitoring glucose prediction algorithms.

BACKGROUND Continuous glucose monitoring (CGM) data can be exploited to prevent hypo-/hyperglycemic events in real time by forecasting future glucose levels. In the last few years, several glucose prediction algorithms have been proposed, but how to compare them (e.g., methods based on polynomial rather than autoregressive time-series models) and even how to determine the optimal parameter set for a given method (e.g., prediction horizon and forgetting) are open problems. METHODS A new index, J, is proposed to optimally design a prediction algorithm by taking into account two key components: the regularity of the predicted profile and the time gained thanks to prediction. Effectiveness of J is compared with previously proposed criteria such as the root mean square error (RMSE) and continuous glucose-error grid analysis (CG-EGA) on 20 Menarini (Florence, Italy) Glucoday® CGM data sets. RESULTS For a given prediction algorithm, the new index J is able to suggest a more consistent and better parameter set (e.g., prediction horizon and forgetting factor of choice) than RMSE and CG-EGA. In addition, the minimization of J can reliably be used as a selection criterion in comparing different prediction methods. CONCLUSIONS The new index can be used to compare different prediction strategies and to optimally design their parameters.
Guaranteed-Stable Sliding DFT Algorithm With Minimal Computational Requirements

The discrete Fourier transform (DFT) is the most widely used technique for determining the frequency spectra of digital signals. However, in the sliding transform scenario where the transform window is shifted one sample at a time and the transform process is repeated, the use of DFT becomes difficult due to its heavy computational burden. This paper proposes an optimal sliding DFT (oSDFT) algorithm that achieves both the lowest computational requirement and the highest computational accuracy among existing sliding DFT algorithms. The proposed oSDFT algorithm directly computes the DFT bins of the shifted window by simply adding (or subtracting) the bins of a previous window and an updating vector. We show that the updating vector can be efficiently computed with a low complexity in the sliding transform scenario. Our simulations demonstrate that the proposed algorithm outperforms the existing sliding DFT algorithms in terms of computational accuracy and processing time.
Interest classification of Twitter users using Wikipedia

We present a framework for (automatically) classifying the relative interests of Twitter users using information from Wikipedia. Our proposed framework first uses Wikipedia to automatically classify a user's celebrity followings into various interest categories, followed by determining the relative interests of the user with a weighting compared to his/her other interests. Our preliminary evaluation on Twitter shows that this framework is able to correctly classify users' interests and that these users frequently converse about topics that reflect both their (detected) interest and a related real-life event.
Who's Speaking?: Audio-Supervised Classification of Active Speakers in Video

Active speakers have traditionally been identified in video by detecting their moving lips. This paper demonstrates the same using spatio-temporal features that aim to capture other cues: movement of the head, upper body and hands of active speakers. Speaker directional information, obtained using sound source localization from a microphone array is used to supervise the training of these video features.
Uncovering pain in critically ill non-verbal children: Nurses’ clinical experiences in the paediatric intensive care unit

Critically ill paediatric patients are frequently exposed to pain that is required to be assessed and treated effectively. The most reliable resource for assessing pain is the child itself, but children in the paediatric intensive care unit (PICU) are commonly unable to communicate their needs, requiring professional caregivers to uncover and interpret pain. However, nurses and paediatricians do not have sufficient knowledge of how critical illness affects childrens’ signs of pain. The aim of this study was to illuminate clinical experiences of pain in the PICU; describing nurses’ perceptions of expressions of pain in non-verbal, critically ill 2—6 year old children. The participants were 17 experienced PICU nurses. Data were analysed according to the phenomenographic method and three qualitatively different main categories, gained from clinical experience, emerged: changes in the measurable parameters; perceived muscular tension; and, altered behaviour. Furthermore, contrasting the categories revealed two diverse perspectives to focus pain: measure-oriented and patient-oriented. Subtle expressions of pain were recognised when focus was patient-oriented. These findings support the necessity of actively looking for pain deriving from various perspectives and considering diverse caring needs when doing so. Acknowledging pain makes pain visible.
Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

Resistance against diseases affects profitability of rainbow trout. Limited information is available about functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for genomic selection. RNA-Seq sequencing of the rainbow trout spleen yielded 93,532,200 reads (100 bp). High quality reads were assembled into 43,047 contigs. 26,333 (61.17%) of the contigs had hits to the NR protein database and 7024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (51%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related genes. KEGG annotation revealed 2825 sequences belonging to “organismal systems” with the highest number of sequences, 842 (29.81%), assigned to immune system. A number of sequences were identified for the first time in rainbow trout belonging to Toll-like receptor signaling (35), B cell receptor signaling pathway (44), T cell receptor signaling pathway (56), chemokine signaling pathway (73), Fc gamma R-mediated phagocytosis (52), leukocyte transendothelial migration (60) and NK cell mediated cytotoxicity (42). In addition, 51 transcripts were identified as spleen-specific genes. The list includes 277 full-length cDNAs. The presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish are conserved. This study provides deep-sequence data of rainbow trout spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help identify allelic variations suitable for genomic selection and genetic manipulation in aquaculture.
Baseline coral disease surveys within three marine parks in Sabah, Borneo

Two of the most significant threats to coral reefs worldwide are bleaching and disease. However, there has been a scarcity of research on coral disease in South-East Asia, despite the high biodiversity and the strong dependence of local communities on the reefs in the region. This study provides baseline data on coral disease frequencies within three national parks in Sabah, Borneo, which exhibit different levels of human impacts and management histories. High mean coral cover (55%) and variable disease frequency (mean 0.25 diseased colonies m−2) were found across the three sites. Highest disease frequency (0.44 diseased colonies per m2) was seen at the site closest to coastal population centres. Bleaching and pigmentation responses were actually higher at Sipadan, the more remote, offshore site, whereas none of the other coral diseases detected in the other two parks were detected in Sipadan. Results of this study offer a baseline dataset of disease in these parks and indicate the need for continued monitoring, and suggest that coral colonies in parks under higher anthropogenic stressors and with lower coral cover may be more susceptible to contracting disease.
Dog is a dog is a dog : Infant rule learning is not specific to language

Human infants possess powerful learning mechanisms used for the acquisition of language. To what extent are these mechanisms domain specific? One well-known infant language learning mechanism is the ability to detect and generalize rule-like similarity patterns, such as ABA or ABB [Marcus, G. F. , Vijayan, S. , Rao, S. B. , & Vishton, P. M. (1999). Rule learning by seven-month-old infants. Science, 283, 77–80. ]. The results of three experiments demonstrate that 7-month-old infants can detect and generalize these same patterns when the elements consist of pictures of animals (dogs and cats). These findings indicate that rule learning of this type is not specific to language acquisition. 2006 Elsevier B.V. All rights reserved.
Lymph node micrometastases of adenocarcinoma located in gastroesophagal junction.

BACKGROUND The aim of this study was to evaluate the presence of micrometastases (MM) and tumor cell microinvolvement (TCM) in regional lymph nodes of patients with gastroesophageal junction adenocarcinoma. MATERIAL AND METHODS 61 patients with adenocarcinoma (stage N0) were included in this study. Lymph nodes removed during surgery were examined using mixed monoclonal antibodies against pan-cytokeratins (AE1/AE3). Micrometastases was defined as single neoplastic cells or infiltration with diameter below 0.5 mm but not involving the interstitium. RESULTS Micrometastases were found in 2 cases with adenocarcinoma type I and 4 cases with type III. Tumor cell microinvolvement was found in 2 cases of either adenocarcinoma type I or type III (according to Siewert's classification). Presence of MM did not influence survival rate. CONCLUSIONS Despite no influence of MM presence on survival rate, MM came from adenocarcinoma type III more frequently. The presence of MM proved lack of homogeneity in the group of N0 stage and makes evaluation advantageous.
Dynamics of Gray Matter Loss in Alzheimer's Disease

We detected and mapped a dynamically spreading wave of gray matter loss in the brains of patients with Alzheimer's disease (AD). The loss pattern was visualized in four dimensions as it spread over time from temporal and limbic cortices into frontal and occipital brain regions, sparing sensorimotor cortices. The shifting deficits were asymmetric (left hemisphere > right hemisphere) and correlated with progressively declining cognitive status (p< 0.0006). Novel brain mapping methods allowed us to visualize dynamic patterns of atrophy in 52 high-resolution magnetic resonance image scans of 12 patients with AD (age 68.4 ± 1.9 years) and 14 elderly matched controls (age 71.4 ± 0.9 years) scanned longitudinally (two scans; interscan interval 2.1 ± 0.4 years). A cortical pattern matching technique encoded changes in brain shape and tissue distribution across subjects and time. Cortical atrophy occurred in a well defined sequence as the disease progressed, mirroring the sequence of neurofibrillary tangle accumulation observed in cross sections at autopsy. Advancing deficits were visualized as dynamic maps that change over time. Frontal regions, spared early in the disease, showed pervasive deficits later (>15% loss). The maps distinguished different phases of AD and differentiated AD from normal aging. Local gray matter loss rates (5.3 ± 2.3% per year in AD v 0.9 ± 0.9% per year in controls) were faster in the left hemisphere (p < 0.029) than the right. Transient barriers to disease progression appeared at limbic/frontal boundaries. This degenerative sequence, observed in vivo as it developed, provides the first quantitative, dynamic visualization of cortical atrophic rates in normal elderly populations and in those with dementia.
Comparative Transcriptome Analysis of Climacteric Fruit of Chinese Pear (Pyrus ussuriensis) Reveals New Insights into Fruit Ripening

The fruit of Pyrus ussuriensis is typically climacteric. During ripening, the fruits produce a large amount of ethylene, and their firmness drops rapidly. Although the molecular basis of climacteric fruit ripening has been studied in depth, some aspects remain unclear. Here, we compared the transcriptomes of pre- and post-climacteric fruits of Chinese pear (P. ussuriensis c.v. Nanguo) using RNA-seq. In total, 3,279 unigenes were differentially expressed between the pre- and post-climacteric fruits. Differentially expressed genes (DEGs) were subjected to Gene Ontology analysis, and 31 categories were significantly enriched in the groups ‘biological process’, ‘molecular function’ and ‘cellular component’. The DEGs included genes related to plant hormones, such as ethylene, ABA, auxin, GA and brassinosteroid, and transcription factors, such as MADS, NAC, WRKY and HSF. Moreover, genes encoding enzymes related to DNA methylation, cytoskeletal proteins and heat shock proteins (HSPs) showed differential expression between the pre- and post-climacteric fruits. Select DEGs were subjected to further analysis using quantitative RT-PCR (qRT-PCR), and the results were consistent with those of RNA-seq. Our data suggest that in addition to ethylene, other hormones play important roles in regulating fruit ripening and may interact with ethylene signaling during this process. DNA methylation-related methyltransferase and cytoskeletal protein genes are also involved in fruit ripening. Our results provide useful information for future research on pear fruit ripening.
ELDERBERRY AND BLACK LOCUST BARK LECTINS

Elderberry (Sambucus nigra) and black locust (Robiniapseudoacacia) agglutinins, which are abundantly present in the bark of both species, display seasonal fluctuations with regard to their content in this tissue. These seasonal changes result apparently from a circa-annual rhythm of lectin accumulation and depletion during autumn and spring, respectively. Because the bark of trees can be considered as a type of vegetative storage tissue, the results suggest that bark lectins behave as typical storage proteins.
Morphologic features of prostatic adenocarcinoma on ThinPrep® urinary cytology

Malignant cells of prostatic adenocarcinoma are rarely identified in urine. In most cases, this finding is associated with high stage tumor. Numerous descriptions of the morphology of prostatic adenocarcinoma have been reported using cytocentrifugated specimens. However, no specific morphologic description of prostatic adenocarcinoma in urine using liquid‐based cytology has been previously described. Four cases of prostatic adenocarcinoma in urine using ThinPrep® liquid‐based preparations were identified between 2002 and 2009 at the University of Wisconsin Hospital and Clinics. Three patients had either high stage tumor or metastatic disease at the time of diagnosis, while the remaining patient had low stage tumor. The morphology of each case was evaluated with specific attention to cell size, nuclear characteristics, nuclear to cytoplasmic ratio, and cytoplasmic characteristics. The resulting key features for prostatic adenocarcinoma in urine are clustering, increased nuclear to cytoplasmic ratio, and prominent nucleoli. Though typically the presence of prostatic adenocarcinoma in urine implies high stage tumor, cells of lower stage tumors may be seen in urine as well. Diagn. Cytopathol. 2011;39:101–104. © 2010 Wiley‐Liss, Inc.
Construction of an ROBDD for a PB-Constraint in Band Form and Related Techniques for PB-Solvers

SUMMARY Pseudo-Boolean (PB) problems are Integer Linear Prob-lem restricted to 0-1 variables. This paper discusses on acceleration techniques of PB-solvers that employ SAT-solving of combined CNFs each of which is produced from each PB-constraint via a binary decision diagram (BDD). Speciﬁcally, we show (i) an e ﬃ cient construction of a reduced ordered BDD (ROBDD) from a constraint in band form l ≤ (cid:3) Linear term (cid:4) ≤ h , (ii) a CNF coding that produces two clauses for some nodes in an ROBDD obtained by (i), and (iii) an incremental SAT-solving of the binary / alternative search for minimizing values of a given goal function. We implemented the proposed constructions and report on experimental re-sults. key words: reduced ordered BDD, Pesudo-Boolean constraint, optimization
Rapid evolution of cold tolerance in stickleback

Climate change is predicted to lead to increased average temperatures and greater intensity and frequency of high and low temperature extremes, but the evolutionary consequences for biological communities are not well understood. Studies of adaptive evolution of temperature tolerance have typically involved correlative analyses of natural populations or artificial selection experiments in the laboratory. Field experiments are required to provide estimates of the timing and strength of natural selection, enhance understanding of the genetics of adaptation and yield insights into the mechanisms driving evolutionary change. Here, we report the experimental evolution of cold tolerance in natural populations of threespine stickleback fish (Gasterosteus aculeatus). We show that freshwater sticklebacks are able to tolerate lower minimum temperatures than marine sticklebacks and that this difference is heritable. We transplanted marine sticklebacks to freshwater ponds and measured the rate of evolution after three generations in this environment. Cold tolerance evolved at a rate of 0.63 haldanes to a value 2.5°C lower than that of the ancestral population, matching values found in wild freshwater populations. Our results suggest that cold tolerance is under strong selection and that marine sticklebacks carry sufficient genetic variation to adapt to changes in temperature over remarkably short time scales.