Miracle-dz/UniFAR-FTUs huggingface dataset:
Meeting the needs of underserved populations: setting the agenda for more inclusive citizen science of medicine

In its expansion to genomic, epidemiological and biomedical research, citizen science has been promoted as contributing to the democratisation of medical research and healthcare. At the same time, it has been criticised for reinforcing patterns of exclusion in health and biomedicine, and sometimes even creating new ones. Although citizen science has the potential to make biomedical research more inclusive, the benefits of current citizen science initiatives are not equally accessible for all people—in particular those who are resource-poor, located outside of traditional networks of healthcare services, or members of minorities and marginalised groups. In view of growing public investments in participatory research endeavours, we argue that it should be considered more explicitly if, and how, citizen science could help make research more inclusive, contribute to the public good, and possibly even lead to better and more equitable healthcare. Reflecting on emerging ethical concerns for scientific conduct and best medical practice, we propose a set of relevant considerations for researchers, practitioners, bioethicists, funders and participants who seek to advance ethical practices of citizen-led health initiatives, and address profound differences in position, privilege and power in research.
The Research Based on H.264 Embedded Video Systems of Optimized Compression Algorithm

Analyzes the basic principles of H.264 video compression algorithm, such as integer DCT, multiple reference frame motion estimation, intra prediction, inter prediction; describes the characteristics of embedded systems, propose a feasible method of video signal optimization, by comparing with the experimental results, the influence of the H.264 coding bit rate bottleneck optimization function obtains a good result. These methods and ideas have practical significance, and it provides a strong reference for other development of video systems.
Cope's Rule in a modular organism: Directional evolution without an overarching macroevolutionary trend

Cope's Rule describes increasing body size in evolutionary lineages through geological time. This pattern has been documented in unitary organisms but does it also apply to module size in colonial organisms? We address this question using 1169 cheilostome bryozoans ranging through the entire 150 million years of their evolutionary history. The temporal pattern evident in cheilostomes as a whole shows no overall change in zooid (module) size. However, individual subclades show size increases: within a genus, younger species often have larger zooids than older species. Analyses of (paleo)latitudinal shifts show that this pattern cannot be explained by latitudinal effects (Bergmann's Rule) coupled with younger species occupying higher latitudes than older species (an “out of the tropics” hypothesis). While it is plausible that size increase was linked to the advantages of large zooids in feeding, competition for trophic resources and living space, other proposed mechanisms for Cope's Rule in unitary organisms are either inapplicable to cheilostome zooid size or cannot be evaluated. Patterns and mechanisms in colonial organisms cannot and should not be extrapolated from the better‐studied unitary organisms. And even if macroevolution simply comprises repeated rounds of microevolution, evolutionary processes occurring within lineages are not always detectable from macroevolutionary patterns.
GATA6 mutations: Characterization of two novel patients and a comprehensive overview of the GATA6 genotypic and phenotypic spectrum

The first human mutations in GATA6 were described in a cohort of patients with persistent truncus arteriosus, and the phenotypic spectrum has expanded since then. This study underscores the broad phenotypic spectrum by presenting two patients with de novo GATA6 mutations, both exhibiting complex cardiac defects, pancreatic, and other abnormalities. Furthermore, we provided a detailed overview of all published human genetic variation in/near GATA6 published to date and the associated phenotypes (n = 78). We conclude that the most common phenotypes associated with a mutation in GATA6 were structural cardiac and pancreatic abnormalities, with a penetrance of 87 and 60%, respectively. Other common malformations were gallbladder agenesis, congenital diaphragmatic hernia, and neurocognitive abnormalities, mostly developmental delay. Fifty‐eight percent of the mutations were de novo, and these patients more often had an anomaly of intracardiac connections, an anomaly of the great arteries, and hypothyroidism, compared with those with inherited mutations. Functional studies mostly support loss‐of‐function as the pathophysiological mechanism. In conclusion, GATA6 mutations give a wide range of phenotypic defects, most frequently malformations of the heart and pancreas. This highlights the importance of detailed clinical evaluation of identified carriers to evaluate their full phenotypic spectrum.
eIF4G1 and carboxypeptidase E axis dysregulation in O-GlcNAc transferase–deficient pancreatic β-cells contributes to hyperproinsulinemia in mice

An early hallmark of type 2 diabetes is a failure of proinsulin-to-insulin processing in pancreatic β-cells, resulting in hyperproinsulinemia. Proinsulin processing is quite sensitive to nutrient flux, and β-cell–specific deletion of the nutrient-sensing protein modifier OGlcNAc transferase (βOGTKO) causes β-cell failure and diabetes, including early development of hyperproinsulinemia. The mechanisms underlying this latter defect are unknown. Here, using several approaches, including site-directed mutagenesis, Click O-GlcNAc labeling, immunoblotting, and immunofluorescence and EM imaging, we provide the first evidence for a relationship between the O-GlcNAcylation of eukaryotic translation initiation factor 4γ1 (eIF4G1) and carboxypeptidase E (CPE)-dependent proinsulin processing in βOGTKO mice. We first established that βOGTKO hyperproinsulinemia is independent of age, sex, glucose levels, and endoplasmic reticulum–CCAAT enhancer-binding protein homologous protein (CHOP)–mediated stress status. Of note, OGT loss was associated with a reduction in β-cell–resident CPE, and genetic reconstitution of CPE in βOGTKO islets rescued the dysfunctional proinsulin-to-insulin ratio. We show that although CPE is not directly OGlcNAc modified in islets, overexpression of the suspected OGT target eIF4G1, previously shown to regulate CPE translation in β-cells, increases islet CPE levels, and fully reverses βOGTKO islet-induced hyperproinsulinemia. Furthermore, our results reveal that OGT O-GlcNAc-modifies eIF4G1 at Ser-61 and that this modification is critical for eIF4G1 protein stability. Together, these results indicate a direct link between nutrient-sensitive OGT and insulin processing, underscoring the importance of post-translational O-GlcNAc modification in general cell physiology.
Constructing a Rule Engine System with SQL Server 2008

Rules play a central role in a wide variety of applications. In addition to the declarative specification of business rules, the simple rule engine design described in this article can be used to implement state machines, predicate dispatchers, or any other rule-based system. This paper introduces how to design a Rule Engine System with SQL Server 2008.
Activation of HIF-1α by δ-Opioid Receptors Induces COX-2 Expression in Breast Cancer Cells and Leads to Paracrine Activation of Vascular Endothelial Cells

Opioids promote tumor angiogenesis in mammary malignancies, but the underlying signaling mechanism is largely unknown. The current study investigated the hypothesis that stimulation of δ-opioid receptors (DOR) in breast cancer (BCa) cells activates the hypoxia-inducible factor 1α (HIF-1α), which triggers synthesis and release of diverse angiogenic factors. Immunoblotting revealed that incubation of human MCF-7 and T47D breast cancer cells with the DOR agonist d-Ala2,d-Leu5-enkephalin (DADLE) resulted in a transient accumulation and thus activation of HIF-1α. DADLE-induced HIF-1α activation preceded PI3K/Akt stimulation and was blocked by the DOR antagonist naltrindole and naloxone, pertussis toxin, different phosphoinositide 3-kinase (PI3K) inhibitors, and the Akt inhibitor Akti-1/2. Whereas DADLE exposure had no effect on the expression and secretion of vascular endothelial growth factor (VEGF) in BCa cells, an increased abundance of cyclooxygenase-2 (COX-2) and release of prostaglandin E2 (PGE2) was detected. DADLE-induced COX-2 expression was also observed in three-dimensional cultured MCF-7 cells and impaired by PI3K/Akt inhibitors and the HIF-1α inhibitor echinomycin. Supernatant from DADLE-treated MCF-7 cells triggered sprouting of endothelial (END) cells, which was blocked when MCF-7 cells were pretreated with echinomycin or the COX-2 inhibitor celecoxib. Also no sprouting was observed when END cells were exposed to the PGE2 receptor antagonist PF-04418948. The findings together indicate that DOR stimulation in BCa cells leads to PI3K/Akt-dependent HIF-1α activation and COX-2 expression, which trigger END cell sprouting by paracrine activation of PGE2 receptors. These findings provide a potential mechanism of opioid-driven tumor angiogenesis and thus therapeutic targets to combat the tumor-angiogenic opioid effect. SIGNIFICANCE STATEMENT Opioids are indispensable analgesics for treating cancer-related pain. However, opioids were found to promote tumor growth and metastasis, which questions the use of these potent pain-relieving drugs in cancer patients. Enhanced tumor vascularization after opioid treatment implies that tumor progression results from angiogenic opioid effects. Thus, understanding the signaling mechanism of opioid-driven tumor angiogenesis helps to identify therapeutic targets to combat these undesired tumor effects. The present study reveals that stimulation of δ-opioid receptors in breast cancer cells leads to an activation of HIF-1α and expression of COX-2 via PI3K/Akt stimulation, which results in a paracrine activation of vascular endothelial cells by prostaglandin E2 receptors.
Stochastic data association in multi-target filtering

Multi-target filtering for closely-spaced targets leads to degraded performance with respect to single-target filtering solutions, due to measurement provenance uncertainty. Soft data association approaches like the probabilistic data association filter (PDAF) suffer track coalescence. Conversely, hard data association approaches like multiplehypothesis tracking (MHT) suffer track repulsion. We introduce the stochastic data association filter (SDAF) that utilizes the PDAF weights in a stochastic, hard data association update step. We find that the SDAF outperforms the PDAF, though it does not match the performance of the MHT solution. We compare as well to the recentlyintroduced equivalence-class MHT (ECMHT) that successfully counters the track repulsion effect. Simulation results are based on the steady-state form of the Ornstein-Uhlenbeck process, allowing for lengthy stochastic realizations with closely-spaced targets.
Effect of Retail Clinic Use on Continuity of Care Among Medicare Beneficiaries

Purpose: We examined the relationship between retail clinic use and primary care physician (PCP) continuity among Medicare enrollees in the Houston metropolitan area. Methods: We identified retail clinic providers in the study area using a 2015 health care provider database. Medicare claims data from enrollees who received care from retail clinics in 2015 were compared with propensity score-matched sample of enrollees who received no care from retail clinics. Results: There were 2.32 retail clinic visits per 1000 beneficiaries in a month. Approximately 1.3% of Medicare beneficiaries used retail clinics. Retail clinic users were more likely to be aged 65 to 74 years, female, White, and Medicaid ineligible. In multivariable analyses with adjustments for covariates, significant predictors of retail clinic use included having ≥3 chronic conditions (Odds Ratio [OR], 1.53 vs no condition), living within 1 mile of a retail clinic (OR, 2.44 vs living ≥5 miles), and having no PCP (OR, 1.11 vs having PCP). Compared with propensity-matched controls, among enrollees with an identified PCP, likelihood of seeing their PCP (OR, 0.82; 95% CI, 0.73 to 0.93) and continuity of care was lower (0.75 ± 0.33 vs 0.80 ± 0.31) if they had retail clinic visits. Conclusions: Retail clinic use was lower in the elderly population compared with the previously published rate in the younger populations. The lower rate of continuity of care observed among retail clinic users is concerning, especially for those with chronic medical conditions.
Research on the Method of Orthogonal Three-Direction Chain Code Used in Corner Detection of Hand Gesture

This paper describes the research on the method of orthogonal three-direction chain code (3OT) used in corner detection of hand gesture. The research is discussed from two aspects: the main idea of 3OT and the experiments on corner detection for hand gesture images of 26 letters in American Sign Language by using 3OT. Experiment results show that the method has well performance with exact corner detection rate and least false corner’s number.
UNIX License Makes Linux the Last Major Piece of the Puzzle

Abstract: From 1992 to 1994, BSD which was UNIX developed at the University of California, Berkeley (UC Berkeley), found itself involved in a license-related lawsuit filed by ATT it is an open source software with publically available source code that can be freely redistributed. The name "Linux" originally referred to the kernel that makes up the core of the OS, however, entire OSs based on the Linux kernel are commonly referred to as Linux.Linux holds only a small share in the desktop PC market where accumulation and continuity of application software is critical. However, in the server OS market Linux competes with the likes of UNIX, represented by Solaris from Sun Microsystems,1 and with Windows Server from Microsoft, the reigning champion of the desktop PC market. The success of Linux made the term "open source" popular worldwide.Since its first official announcement by Linus Benedict Torvalds in October of 1991, Linux has been evolving at an astounding pace, achieving superior functionality in its lightness, high degree of freedom, and reliability. A few years later, in 1995, it was being used as a practical and stable OS (Leibovitch, 1999). At that time, Microsoft founder Bill Gates' famous "An Open Letter to Hobbyists"2 would epitomize source codes to be protected as intellectual property with usage rights to be granted to consumers for a fee. In the midst of this, Linux was provided free of charge and its source code was made publically available. These practices were greeted with surprise and sympathy, and considered as the reason for its success along with intuitive discussions (e.g., DiBona, Ockman, & Stone, 1999). Furthermore, for-profit enterprises such as Netscape, Apple, Hewlett Packard, and IBM subsequently began publicizing their adoption of the open source strategy, making their source codes available to the public (Hamerly, Pazuin, & Walton, 1999; Landry, 2000). However, the open source strategies of these for-profit enterprises were not as successful as that of Linux. The definitive reason for the success of Linux was in its miraculously perfect entry that filled the gaps left by preceding groups. This phenomenon could not be repeated even under ideal conditions of it being free of charge and open source.2. The Birth of UNIXUNIX was developed at ATT he rewrote the entire system for it to operate like an OS (Salus, 1994, chap. 1). This small-scale, light, and user-friendly OS was called UNICS, which later became UNIX.The first edition of the UNIX Programmer's Manual was published jointly by Thompson and Ritchie on November 3, 1971 to be used with the PDP-11/20 (Salus, 1994, chap. 13). The PDP-11 series hardware was quite limited in address and memory, which brought about a prominent characteristic of UNIX. …
Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches.

Trebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free-living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all OTUs, however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as Trebouxia, Myrmecia and Symbiochloris were also abundantly detected in the ocean, suggesting either free-living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean. This article is protected by copyright. All rights reserved.
Optimizing a Noninvasive Oral Sampling Technique for Semicaptive Neotropical Primates in Peru

Abstract: Disease surveillance in Neotropical primates (NP) is limited by the difficulties associated with anesthetizing NP for sample collection in remote settings. Our objective was to optimize a noninvasive method of oral sampling from semicaptive NP in Peru. We offered 40 NP at Taricaya Rescue Centre in Madre de Dios, Peru ropes coated in various attractants and measured variables (acceptance of the rope, chewing time, and volume of fluid eluted from ropes) that may affect sample acquisition and quality. We preserved samples by direct freezing in liquid nitrogen or by storing samples in RNA stabilization reagent at room temperature. Sample integrity was measured by testing for mammalian cytochrome b with the use of conventional PCR. The NP successfully chewed on a rope in 82% (125/152) of trials. Overall sample integrity was high, with 96% (44/46) of samples (both directly frozen and stored in stabilization reagent) testing positive for cytochrome b. The number of times that an individual NP was exposed to the rope procedure and NP age were associated with higher acceptance rates and the NP successfully chewing on the rope. We conclude that ropes serve as a feasible noninvasive method of obtaining oral samples from NP at rescue centers and could be used in future studies to evaluate population genetics and for pathogen surveillance for population health monitoring.
Allocation to groups: Examples of Lord's paradox.

Educational and developmental psychologists often examine how groups change over time. Two analytic procedures - analysis of covariance (ANCOVA) and the gain score model - each seem well suited for the simplest situation, with just two groups and two time points. They can produce different results, what is known as Lord's paradox. Several factors should influence a researcher's analytic choice. This includes whether the score from the initial time influences how people are assigned to groups. Examples are shown, which will help to explain this to researchers and students, and are of educational relevance. It is shown that a common method used to measure school effectiveness is biased against schools that serve students from groups that are historically poor performing. The examples come from sports and measuring educational effectiveness (e.g., for teachers or schools). A simulation study shows that if the covariate influences group allocation, the ANCOVA is preferred, but otherwise, the gain score model may be appropriate. Regression towards the mean is used to account for these findings. Analysts should consider the relationship between the covariate and group allocation when deciding upon their analytic method. Because the influence of the covariate on group allocation may be complex, the appropriate method may be complex. Because the influence of the covariate on group allocation may be unknown, the choice of method may require several assumptions.
The Design and Implementation of SPARK, a Toolkit for Implementing Domain-Specific Languages

SPARK is a toolkit for implementing domain-specific languages in Python. It is somewhat unusual in that its intended audience includes users who do not necessarily have a background in compilation; this choice impacts both the design and implementation of SPARK. We introduce SPARK in this paper and discuss major issues that have arisen in its design and ongoing development.
Fully transparent orthography, yet lexical reading aloud: The lexicality effect in Italian

This is the first study that reports the lexicality effect (i.e., words read better than nonwords) in Italian with fully transparent and methodologically well-controlled stimuli. We investigated how words and nonwords are read aloud in the Italian transparent orthography, in which there is an almost strict one-to-one correspondence between graphemes and phonemes. Contrary to the claim that in such orthography word naming is accomplished primarily by the nonlexical assembly route, we found that words were named faster than nonwords, regardless of their frequency (high or low) or the composition of the experimental list (pure vs. mixed blocks). These findings show that the lexical route is the main one used by readers even in a language with a transparent orthography.
The structure of the extended E2 DNA‐binding domain of the bovine papillomavirus‐1

Bovine papillomavirus proteins were extensively studied as a prototype for the human papillomavirus. Here, the crystal structure of the extended E2 DNA‐binding domain of the dominant transcription regulator from the bovine papillomavirus strain 1 is described in the space group P3121. We found two protein functional dimers packed in the asymmetric unit. This new protein arrangement inside the crystal led to the reduction of the mobility of a previously unobserved loop directly involved in the protein‐DNA interaction, which was then modeled for the first time.