Miracle-dz/UniFAR-FTUs huggingface dataset:
Local cell interactions and self-amplifying individual cell ingression drive amniote gastrulation

Gastrulation generates three layers of cells (ectoderm, mesoderm, endoderm) from a single sheet, while large scale cell movements occur across the entire embryo. In amniote (reptiles, birds, mammals) embryos, the deep layers arise by epithelial-to-mesenchymal transition (EMT) at a morphologically stable midline structure, the primitive streak (PS). We know very little about how these events are controlled or how the PS is maintained despite its continuously changing cellular composition. Using the chick, we show that isolated EMT events and ingression of individual cells start well before gastrulation. A Nodal-dependent ‘community effect’ then concentrates and amplifies EMT by positive feedback to form the PS as a zone of massive cell ingression. Computer simulations show that a combination of local cell interactions (EMT and cell intercalation) is sufficient to explain PS formation and the associated complex movements globally across a large epithelial sheet, without the need to invoke long-range signalling. DOI: http://dx.doi. org/10.7554/eLife.01817. 001
Integrated Approach to Conceptual Modeling

Conceptual modeling is supporting understanding and communication of the requirements in developing the information system (IS). The nature of requirements is usually divided into the functional (FRs) and non-functional requirements (NFRs). Thus, the scholars who are representing the conceptual modeling separate FRs and NFRs. Attempting to create an integrated framework for conceptual modeling of FRs and NFRs a new approach is being represented. In order to justify the approach, the research work and relevant literature in the field by using integrated perspective has been analyzed in this paper. As an outcome of this review, the need for an integrated approach to the requirement determination and proposed an integrated framework for conceptual modeling, which shall include the functional and non-functional requirements in one conceptual model has been identified. There is also identified that a small number of researchers have worked in this field, whilst the failure rate of the IS implementation which continues to be high has been the motivation, therefore the concept of proposing an integrated framework which will contribute to the increase of the efficacy of the requirements from the analysis phase in order to secure the sustainability of the IS has been approached.
An Evaluation of the Frankfort Mandibular Plane Angle Bisector (FMAB) Wits Appraisal in the Assessment of Anteroposterior Jaw Relationships

An accurate anteroposterior measurement of jaw relationships is essential in orthodontic diagnosis and treatment planning. The purpose of this longitudinal study was to establish a new cephalometric Wits appraisal using a bisector of the mandibular plane angle, named the Frankfort Mandibular Plane Angle Bisector (FMAB). The FMAB was used to assess the sagittal jaw relationship in a sample of Class I individuals, and compare this measurement to the ANB angle and the Wits appraisal using the Maxillomandibular Bisector (MMB). The data were collected from pre-treatment (T0), immediate post-treatment (T1) and two year post-retention (T2) lateral cephalograms of 61 male and 60 female Class I subjects. Non-extraction, fixed orthodontic appliance treatment in the permanent dentition was carried out for these patients. Cephalometric data were compared to 19 male and 19 female Class I subjects who had no orthodontic treatment and served as controls. The FMAB was determined to be a reproducible reference plane which undergoes change in response to growth and treatment, consistent with the changes seen in the ANB angle. A good correlation (r>0.86) was found between the MMB and FMAB Wits appraisal measurements in both the control and treatment groups for all time periods, indicating that the use of either of these measures may be indicated in cephalometric analysis. Key Words: Wits Appraisal, Frankfort Mandibular Plane Bisector, Anteroposterior Skeletal Discrepancy
Link between Aluminum and the Pathogenesis of Alzheimer's Disease: The Integration of the Aluminum and Amyloid Cascade Hypotheses

Whilst being environmentally abundant, aluminum is not essential for life. On the contrary, aluminum is a widely recognized neurotoxin that inhibits more than 200 biologically important functions and causes various adverse effects in plants, animals, and humans. The relationship between aluminum exposure and neurodegenerative diseases, including dialysis encephalopathy, amyotrophic lateral sclerosis and Parkinsonism dementia in the Kii Peninsula and Guam, and Alzheimer's disease (AD) has been suggested. In particular, the link between aluminum and Alzheimer's disease has been the subject of scientific debate for several decades. However, the complex characteristics of aluminum bioavailability make it difficult to evaluate its toxicity and therefore, the relationship remains to be established. Mounting evidence has suggested that significance of oligomerization of β-amyloid protein and neurotoxicity in the molecular mechanism of AD pathogenesis. Aluminum may play crucial roles as a cross-linker in β-amyloid oligomerization. Here, we review the detailed characteristics of aluminum neurotoxicity based on our own studies and the recent literatures. Our aim is to revisit the link between aluminum and AD and to integrate aluminum and amyloid cascade hypotheses in the context of β-amyloid oligomerization and the interactions with other metals.
Intelligent Residential Air-Conditioning System With Smart-Grid Functionality

This paper sets forth a novel intelligent residential air-conditioning (A/C) system controller that has smart grid functionality. The qualifier “intelligent” means the A/C system has advanced computational capabilities and uses an array of environmental and occupancy parameters in order to provide optimal intertemporal comfort/cost trade-offs for the resident, conditional on anticipated retail energy prices. The term “smart-grid functionality” means that retail energy prices can depend on wholesale energy prices. Simulation studies are used to demonstrate the capabilities of the proposed A/C system controller.
Evolutionary dynamics of a multi-trait semelparous model

We consider a multi-trait evolutionary (game theoretic) version of a two class (juvenile-adult) semelparous Leslie model. We prove the existence of both a continuum of positive equilibria and a continuum of synchronous 2-cycles as the result of a bifurcation that occurs from the extinction equilibrium when the net reproductive number $R_{0}$ increases through $1$. We give criteria for the direction of bifurcation and for the stability or instability of each bifurcating branch. Semelparous Leslie models have imprimitive projection matrices. As a result (unlike matrix models with primitive projection matrices) the direction of bifurcation does not solely determine the stability of a bifurcating continuum. Only forward bifurcating branches can be stable and which of the two is stable depends on the intensity of between-class competitive interactions. These results generalize earlier results for single trait models. We give an example that illustrates how the dynamic alternative can change when the number of evolving traits changes from one to two.
A Best Evidence Synthesis of Literacy Instruction on the Social Adjustment of Students With or At-risk for Behavior Disorders

The findings of a best-evidence synthesis of the collateral effect of literacy instruction on the social adjustment of students are reported. The goal of the synthesis was to extend the work of Wanzek, Vaughn, Kim, and Cavanaugh (2006) by (a) reviewing treatment-outcomes conducted using group design methodology; (b) focusing on a more defined set of outcome measures; and (c) analyzing outcomes using average effect size estimates as a common metric. Results of the review suggest that effective literacy instruction does not appear to have a collateral effect on the social adjustment of children. Limitations and future directions are presented.
The role of self-organisation in the emergence of phonological systems

The origin of phonological systems is examined from the paradigm of self-organization. We claim that phonological systems could have emerged as the product of self-organizing processes. Self-organization may have facilitated the evolution of structures within the sounds that humans were able to produce. One of the main points of the paper concerns the identification of the processes which could account for the self-organized behavior of sound systems used in languages spoken by humans. In this paradigm, phonological systems or sound patterns of human languages are emergent properties of these systems rather than properties imposed by some external influence. Regulations are defined as the constraints that adjust the rate of production of the elements of a system to the state of the system and of relevant environmental variables. The main operators of these adjustments are feedback loops. Two types of processes can be distinguished in regulatory networks, homeostatic and epigenetic. Since the origin of sound patterns, of human languages, is in the vocal tract constraints, we make the hypothesis that sound change does not reflect any adaptive character but rather is the phonetic modality of differentiation understood as epigenetic regulation.
Internet privacy

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Development of an MRI-compatible digital SiPM detector stack for simultaneous PET/MRI

Advances in solid-state photon detectors paved the way to combine positron emission tomography (PET) and magnetic resonance imaging (MRI) into highly integrated, truly simultaneous, hybrid imaging systems. Based on the most recent digital SiPM technology, we developed an MRI-compatible PET detector stack, intended as a building block for next generation simultaneous PET/MRI systems. Our detector stack comprises an array of 8 × 8 digital SiPM channels with 4 mm pitch using Philips Digital Photon Counting DPC 3200-22 devices, an FPGA for data acquisition, a supply voltage control system and a cooling infrastructure. This is the first detector design that allows the operation of digital SiPMs simultaneously inside an MRI system. We tested and optimized the MRI-compatibility of our detector stack on a laboratory test bench as well as in combination with a Philips Achieva 3 T MRI system. Our design clearly reduces distortions of the static magnetic field compared to a conventional design. The MRI static magnetic field causes weak and directional drift effects on voltage regulators, but has no direct impact on detector performance. MRI gradient switching initially degraded energy and timing resolution. Both distortions could be ascribed to voltage variations induced on the bias and the FPGA core voltage supply respectively. Based on these findings, we improved our detector design and our final design shows virtually no energy or timing degradations, even during heavy and continuous MRI gradient switching. In particular, we found no evidence that the performance of the DPC 3200-22 digital SiPM itself is degraded by the MRI system.
Psychiatric Comorbidity Among Inpatient Substance Abusing Adolescents

ABSTRACT We studied the association between type, severity and sequencing of psychopathology and these same dimensions of substance involvement among inpatient substance-abusing adolescents with comorbid psychiatric disorders. Adolescents (N = 140, 54% female; 15.9 years) meeting DSM-III-R criteria for a substance use disorder and at least one other Axis I psychiatric disorder were interviewed while inpatients in an adolescent psychiatric facility. Findings point to associations between externalizing disorders and a history of regular use of cigarettes, alcohol, and stimulants among comorbid adolescents. When sequencing of psychopathology was examined, different substance use patterns were observed. Severity of depressive disorders was associated with more substance withdrawal symptoms, externalizing symptomatology was related to more substance dependence symptoms, and ADHD severity was associated with more alcohol dependence symptoms. Findings may have important clinical implications such as the need to assess comorbidity early and to develop treatment plans based on type of comorbid psychiatric disorder.
The complex becomes more complex: protein-protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell- and stimulus type-specific SnRK1 signaling in plants

In plants, SNF1-related kinase (SnRK1) responds to the availability of carbohydrates as well as to environmental stresses by down-regulating ATP consuming biosynthetic processes, while stimulating energy-generating catabolic reactions through gene expression and post-transcriptional regulation. The functional SnRK1 complex is a heterotrimer where the catalytic α subunit associates with a regulatory β subunit and an activating γ subunit. Several different metabolites as well as the hormone abscisic acid (ABA) have been shown to modulate SnRK1 activity in a cell- and stimulus-type specific manner. It has been proposed that tissue- or stimulus-specific expression of adapter proteins mediating SnRK1 regulation can at least partly explain the differences observed in SnRK1 signaling. By using yeast two-hybrid and in planta bi-molecular fluorescence complementation assays we were able to demonstrate that proteins containing the domain of unknown function (DUF) 581 could interact with both isoforms of the SnRK1α subunit (AKIN10/11) of Arabidopsis. A structure/function analysis suggests that the DUF581 is a generic SnRK1 interaction module and co-expression with DUF581 proteins in plant cells leads to reallocation of the kinase to specific regions within the nucleus. Yeast two-hybrid analyses suggest that SnRK1 and DUF581 proteins share common interaction partners inside the nucleus. The analysis of available microarray data implies that expression of the 19 members of the DUF581 encoding gene family in Arabidopsis is differentially regulated by hormones and environmental cues, indicating specialized functions of individual family members. We hypothesize that DUF581 proteins could act as mediators conferring tissue- and stimulus-type specific differences in SnRK1 regulation.
Estimating the unseen: an n/log(n)-sample estimator for entropy and support size, shown optimal via new CLTs

We introduce a new approach to characterizing the unobserved portion of a distribution, which provides sublinear--sample estimators achieving arbitrarily small additive constant error for a class of properties that includes entropy and distribution support size. Additionally, we show new matching lower bounds. Together, this settles the longstanding question of the sample complexities of these estimation problems, up to constant factors. Our algorithm estimates these properties up to an arbitrarily small additive constant, using O(n/log n) samples, where n is a bound on the support size, or in the case of estimating the support size, 1/n is a lower bound on the probability of any element of the domain. Previously, no explicit sublinear--sample algorithms for either of these problems were known. Our algorithm is also computationally extremely efficient, running in time linear in the number of samples used. In the second half of the paper, we provide a matching lower bound of Ω(n/log n) samples for estimating entropy or distribution support size to within an additive constant. The previous lower-bounds on these sample complexities were n/2O(√log n). To show our lower bound, we prove two new and natural multivariate central limit theorems (CLTs); the first uses Stein's method to relate the sum of independent distributions to the multivariate Gaussian of corresponding mean and covariance, under the earthmover distance metric (also known as the Wasserstein metric). We leverage this central limit theorem to prove a stronger but more specific central limit theorem for "generalized multinomial" distributions---a large class of discrete distributions, parameterized by matrices, that represents sums of independent binomial or multinomial distributions, and describes many distributions encountered in computer science. Convergence here is in the strong sense of statistical distance, which immediately implies that any algorithm with input drawn from a generalized multinomial distribution behaves essentially as if the input were drawn from a discretized Gaussian with the same mean and covariance. Such tools in the multivariate setting are rare, and we hope this new tool will be of use to the community.
The Power of a Nod and a Glance: Envelope Vs. Emotional Feedback in Animated Conversational Agents

In this article we describe results froman experiment of user interaction with autonomous , human - like ( humanoid ) conversational agents . We hypothesize that for embodied conversational agents , nonverbal behaviors related to the process of conversation , what we call envelope feedback, is much more important than other feedback , such as emotional expression . We test this hypothesis by having subjects interact with three autonomous agents , all capable of full - duplex multimodal interaction: able to generate and recognize speech , intonation , facial displays , and gesture . Each agent , however , gave a different kind of feedback: ( 1 ) content - related only , ( 2 ) content + envelope feedback , and ( 3 ) content + emotional . Content-related feedback includes answering questions and executing commands; envelope feedback includes behaviors such as gaze , manual beat gesture , and head movements; emotional feedback includes smiles and looks of puzzlement . Subjects' evaluations of the systemwere c.
First Detection of Mycobacterium ulcerans DNA in Environmental Samples from South America

The occurrences of many environmentally-persistent and zoonotic infections are driven by ecosystem changes, which in turn are underpinned by land-use modifications that alter the governance of pathogen, biodiversity and human interactions. Our current understanding of these ecological changes on disease emergence however remains limited. Buruli ulcer is an emerging human skin disease caused by the mycobacterium, Mycobacterium ulcerans, for which the exact route of infection remains unclear. It can have a devastating impact on its human host, causing extensive necrosis of the skin and underlying tissue, often leading to permanent disability. The mycobacterium is associated with tropical aquatic environments and incidences of the disease are significantly higher on floodplains and where there is an increase of human aquatic activities. Although the disease has been previously diagnosed in South America, until now the presence of M. ulcerans DNA in the wild has only been identified in Australia where there have been significant outbreaks and in western and central regions of Africa where the disease is persistent. Here for the first time, we have identified the presence of the aetiological agent's DNA in environmental samples from South America. The DNA was positively identified using Real-time Polymerase Chain Reaction (PCR) on 163 environmental samples, taken from 23 freshwater bodies in French Guiana (Southern America), using primers for both IS2404 and for the ketoreductase-B domain of the M. ulcerans mycolactone polyketide synthase genes (KR). Five samples out of 163 were positive for both primers from three different water bodies. A further nine sites had low levels of IS2404 close to a standard CT of 35 and could potentially harbour M. ulcerans. The majority of our positive samples (8/14) came from filtered water. These results also reveal the Sinnamary River as a potential source of infection to humans.
Errors in meta‐analysis on prevalence of nonalcoholic fatty liver disease

inflammation, insulin resistance, and fibrosis, and whether NAFLD influences CVD risk, diabetes risk, or risk of other extrahepatic complications linked with NAFLD, such as chronic renal disease. We appreciate the authors’ call for more liberal NAFLD screening policies. Based on recent analyses of epidemiological modifiers of NAFLD and preliminary cost-utility analyses, we reached similar conclusions. Individuals belonging to NAFLD high-risk groups warrant screening for fatty liver disease.
Intraoperative hypotension - a neglected causative factor in hospital-acquired acute kidney injury; a Mayo Clinic Health System experience revisited

Acute kidney injury (AKI) is a relatively common complication of cardiothoracic surgery and has both short- and long-term survival implications, even when AKI does not progress to severe renal failure. Given that currently, there are no active effective treatments for AKI, other than renal replacement therapy when indicated, the focus of clinicians ought to be on prevention and risk factor management. In the AKI-surgery literature, there exists this general consensus that intraoperative hypotension (IH) following hypotensive anesthesia (HA) or controlled hypotension (CH) in the operating room has no significant short-term and long-term impacts on renal function. In this review, we examine the basis for this consensus, exposing some of the flaws of the clinical study data upon which this prevailing consensus is based. We then describe our experiences in the last decade at the Mayo Clinic Health System, Eau Claire, in Northwestern Wisconsin, USA, with two selected case presentations to highlight the contribution of IH as a potent yet preventable cause of post-operative AKI. We further highlight the causative although neglected role of IH in precipitating postoperative AKI in chronic kidney disease (CKD) patients. We show additional risk factors associated with this syndrome and further make a strong case for the elimination of IH as an achievable mechanism to reduce overall, the incidence of hospital acquired AKI. We finally posit that as the old saying goes, prevention is indeed better than cure.
Social Inequality and Predatory Criminal Victimization: An Exposition and Test of a Formal Theory

This study systematically tests a formal theory of how certain dimensions of social stratification--income, race, and age--relate to risk of predatory criminal victimization. An opportunity theory of criminal victimization is proposed, focusing on the mediating role played by five risk factors: exposure, guardianship, proximity to potential offenders, attractiveness of potential targets, and definitional properties of specific crimes themselves. Propositions are derived pertaining to the bivariate and multivariate-partial (main) effects expected from the theory and tested in analyses based on a representative sample of the U.S. population for the crimes of assault, burglary, and personal larceny. These data indicate that the relationship between the dimensions of social stratification and the offenses studied here is complex, and that, other things being equal, those usually thought to be most vulnerable economically and socially--the poor, the nonwhite, the old--are not the most likely victims of crime. Race has little direct effect on victimization risk, while age is inversely related to each type of crime at both the bivariate and multivariate levels of analyses. The findings are largely consistent with the proposed theory. (abstract Adapted from Source: American Sociological Review, 1981. Copyright © 1981 by the American Sociological Association) Victimization Causes Crime Victim Violence Victim Racial Factors Age Factors Socioeconomic Factors Victimization Risk Factors 07-02