Miracle-dz/UniFAR-FTUs huggingface dataset:
On the development of the stratification of the inner plexiform layer in the chick retina

This study investigated the development of the subdivision of the chick inner plexiform layer (IPL). The approach included an immunohistological analysis of the temporal and spatial expressions of choline acetyltransferase, of the neural–glial‐related and neural–glial cell adhesion molecules (NrCAM and NgCAM, respectively) and axonin‐1, and of inwardly rectifying potassium (Kir) channels in 5‐ to 19‐day‐old (E5–E19) embryos. Ultrastructural investigations evaluated whether synaptogenesis accompanies the onset of differentiation of the IPL. We found that the differentiation of the IPL started at E9. Distinct cholinergic strata appeared, NrCAM immunoreactivity showed a poorly defined stratification, and Kir3.2 was expressed in the IPL and in the inner nuclear layer. From E10 until late E14, NgCAM‐ and axonin‐1–immunoreactive strata emerged in an alternating sequence from the outer to the inner IPL. During this period, the NrCAM pattern sharpened, and eventually five bands of weaker and stronger immunoreactivity were found. Conventional synapses formed at the beginning of E9, and stratification of the IPL also began on the same day at the same location. Synaptogenesis and stratification followed a gradient from the central to the peripheral retina. The topographic course of differentiation of the IPL generally corresponded to the course of maturation of ganglion and amacrine cells. Synaptogenesis and the expression of G‐protein–gated Kir3.2 channels accompanied the onset of stratification. These events coincide with the occurrence of robust and rhythmic spontaneous neuronal activity. The subsequent differentiation of the IPL seemed to be orchestrated by several mechanisms. J. Comp. Neurol. 460:1–12, 2003. © 2003 Wiley‐Liss, Inc.
Perfluoroalkyl and polyfluoroalkyl substances and human fetal growth: A systematic review

Abstract Background: Exposure to perfluoroalkyl and polyfluoroalkyl substances (PFASs) is ubiquitous in most regions of the world. The most commonly studied PFASs are perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA). Animal studies indicate that maternal PFAS exposure is associated with reduced fetal growth. However, the results of human studies are inconsistent. Objectives: To summarize the evidence of an association between exposure to PFASs, particularly PFOS and PFOA, and human fetal growth. Methods: Systematic literature searches were performed in MEDLINE and EMBASE. We included original studies on pregnant women with measurements of PFOA or PFOS in maternal blood during pregnancy or the umbilical cord and associations with birth weight or related outcomes according to the PFAS level. Citations and references from the included articles were investigated to locate more relevant articles. Study characteristics and results were extracted to structured tables. The completeness of reporting as well as the risk of bias and confounding were assessed. Results: Fourteen studies were eligible. In utero PFOA exposure was associated with decreased measures of continuous birth weight in all studies, even though the magnitude of the association differed and many results were statistically insignificant. PFOS exposure and birth weight were associated in some studies, while others found no association. Conclusions: Higher PFOS and PFOA concentrations were associated with decreased average birth weight in most studies, but only some results were statistically significant. The impact on public health is unclear, but the global exposure to PFASs warrants further investigation.
PEDro or Cochrane to Assess the Quality of Clinical Trials? A Meta-Epidemiological Study

Objective There is debate on how the methodological quality of clinical trials should be assessed. We compared trials of physical therapy (PT) judged to be of adequate quality based on summary scores from the Physiotherapy Evidence Database (PEDro) scale with trials judged to be of adequate quality by Cochrane Risk of Bias criteria. Design Meta-epidemiological study within Cochrane Database of Systematic Reviews. Methods Meta-analyses of PT trials were identified in the Cochrane Database of Systematic Reviews. For each trial PeDro and Cochrane assessments were extracted from the PeDro and Cochrane databases. Adequate quality was defined as adequate generation of random sequence, concealment of allocation, and blinding of outcome assessors (Cochrane criteria) or as trials with a PEDro summary score ≥5 or ≥6 points. We combined trials of adequate quality using random-effects meta-analysis. Results Forty-one Cochrane reviews and 353 PT trials were included. All meta-analyses included trials with PEDro scores ≥5, 37 (90.2%) included trials with PEDro scores ≥6 and only 22 (53.7%) meta-analyses included trials of adequate quality according to the Cochrane criteria. Agreement between PeDro and Cochrane was poor for PeDro scores of ≥5 points (kappa = 0.12; 95% CI 0.07 to 0.16) and slight for ≥6 points (kappa 0.24; 95% CI 0.16-0.32). When combining effect sizes of trials deemed to be of adequate quality according to PEDro or Cochrane criteria, we found that a substantial difference in the combined effect size (≥0.15) was evident in 9 (22%) out of the 41 meta-analyses for PEDro cutoff ≥5 and 10 (24%) for cutoff ≥6. Conclusions The PeDro and Cochrane approaches lead to different sets of trials of adequate quality, and different combined treatment estimates from meta-analyses of these trials. A consistent approach to assessing RoB in trials of physical therapy should be adopted.
The expression of MDM2/CDK4 gene product in the differential diagnosis of well differentiated liposarcoma and large deep-seated lipoma

Ordinary lipomas are cytogenetically characterized by a variety of balanced rearrangements involving chromosome segment 12q13–15, whereas well differentiated liposarcomas (WDL) show supernumerary ring and giant marker chromosomes, known to contain amplified 12q sequences. The tight correlation between the presence of ring chromosomes and both amplification and overexpression of MDM2 and CDK4 genes suggests the exploration of the possibility that immunocytochemistry (ICC) might assist in the differential diagnosis of lipoma-like well differentiated liposarcomas (LL-WDL) and large deep-seated lipomas (LDSL). For this purpose, 21 cases of the former and 19 cases of the latter tumours were analysed by ICC and, according to the availability of material, by molecular and cytogenetic approaches. All lipomas displayed a null MDM2/CDK4 phenotype, whereas all LL-WDL showed MDM2/CDK4 or CDK4 phenotypes. Southern blot analysis performed on 16 suitable cases, complemented by fluorescence in situ hybridization and classical cytogenetic analysis in 11 cases, was consistent with, and further supported the immunophenotyping data. In conclusion, MDM2/CDK4 product-based immunophenotyping appears to represent a valuable method for the categorization of arguable LDSL. © 2000 Cancer Research Campaign
Recommending Recipients in the Enron Email Corpus

Email is the most popular communication tool of the internet. In this paper we investigate how email systems can be enhanced to work as recipient recommendation systems, i.e., suggesting who recipients of a message might be, while the message is being composed, given its current contents and given its previously-specified recipients. This can be a valuable addition to email clients, particularly in large corporations. It can be used to identify people in an organization that are working in a similar topic or project, or to find people with appropriate expertise or skills. Recipient recommendation can also prevent a user from forgetting to add an important collaborator or manager as recipient, preventing costly misunderstandings and communication delays. In this paper we present the first study of recipient recommendation in a real large-scale corporate email collection, the Enron Email corpus. We begin by defining the problem as a large multi-class multi-label classification task, where each email can be addressed to multiple recipients in the user’s address book (i.e., each class is equivalent to an email address in the address book). We propose various baselines to the problem, along with a classification-based reranking scheme to combine two types of features: textual contents and network information from the email headers. Experiments indicate that the reranking scheme significantly outperforms the baselines, and that the best scheme is accurate enough to be useful in email clients. Results are encouraging also because the proposed solution can be easily implemented in any email client – with no changes in the email server side.
SoftAR: Visually Manipulating Haptic Softness Perception in Spatial Augmented Reality

We present SoftAR, a novel spatial augmented reality (AR) technique based on a pseudo-haptics mechanism that visually manipulates the sense of softness perceived by a user pushing a soft physical object. Considering the limitations of projection-based approaches that change only the surface appearance of a physical object, we propose two projection visual effects, i.e., surface deformation effect (SDE) and body appearance effect (BAE), on the basis of the observations of humans pushing physical objects. The SDE visualizes a two-dimensional deformation of the object surface with a controlled softness parameter, and BAE changes the color of the pushing hand. Through psychophysical experiments, we confirm that the SDE can manipulate softness perception such that the participant perceives significantly greater softness than the actual softness. Furthermore, fBAE, in which BAE is applied only for the finger area, significantly enhances manipulation of the perception of softness. We create a computational model that estimates perceived softness when SDE+fBAE is applied. We construct a prototype SoftAR system in which two application frameworks are implemented. The softness adjustment allows a user to adjust the softness parameter of a physical object, and the softness transfer allows the user to replace the softness with that of another object.
Ileal Conduit and Continent Ileocecal Pouch for Patients Undergoing Pelvic Exenteration: Comparison of Complications and Quality of Life

Objectives: Creating a continent urinary pouch has become an alternative to the ileal conduit for patients undergoing exenteration for advanced gynecologic malignancies. The objective of this study was to compare clinical outcomes for the 2 methods. Methods: In this retrospective study, we compared intraoperative and postoperative complications and quality-of-life scores for the modified ileocecal pouch and the ileal conduit in anterior or total pelvic exenteration. Results: In 33 of 100 patients, an ileal pouch (IP) was created; the other 67 were treated by an ileal conduit (IC). Creating an IP prolonged the exenterative procedure by 97 minutes compared to an IC (IC, 453 minutes vs IP, 550 minutes; P = 0.009). Overall complication rates were similar, but patients with an IP had significantly more complications of urinary diversion (48%) than patients with an IC (31%; P = 0.03). Follow-up showed urinary loss and frequency of micturition to be comparable, but in patients with an IP, surgery for stomal complications (n = 2) and treatment of bladderstones were necessary more frequently (n = 3). Quality of life according to the 12-item Short Form Health Survey questionnaire was similar in both groups. Conclusion: A continent IP is an alternative to the IC in cases of pelvic exenteration. Early complications are more frequent with an IP than with an IC. The mode of urinary diversion has little influence on the quality of life in patients with advanced genital cancer.
LHDiff: Tracking Source Code Lines to Support Software Maintenance Activities

Tracking lines across versions of a file is a necessary step for solving a number of problems during software development and maintenance. Examples include, but are not limited to, locating bug-inducing changes, tracking code fragments or vulnerable instructions across versions, co-change analysis, merging file versions, reviewing source code changes, and software evolution analysis. In this tool demonstration, we present a language-independent line-level location tracker, named LHDiff, that can be used to track lines and analyze changes in various kinds of software artifacts, ranging from source code to arbitrary text files. The tool can effectively detect changed or moved lines across versions of a file, has the ability to detect line splits, and can easily be integrated with existing version control systems. It overcomes the limitations of existing language-independent techniques and is even comparable to tools that are language dependent. In addition to describing the tool, we also describe its effectiveness in analyzing source code artifacts.
Grade of Membership Model and Visualization for RNA-seq data using CountClust

Grade of membership or GoM models (also known as admixture models or Latent Dirichlet Allocation”) are a generalization of cluster models that allow each sample to have membership in multiple clusters. It is widely used to model ancestry of individuals in population genetics based on SNP/ microsatellite data and also in natural language processing for modeling documents [1, 3]. This R package implements tools to visualize the clusters obtained from fitting topic models using a Structure plot [2] and extract the top features/genes that distinguish the clusters. In presence of known technical or batch effects, the package also allows for correction of these confounding effects. CountClust version: 1.2. 0 1 This document used the vignette from Bioconductor package DESeq2, cellTree as knitr template
Metacognition and Cognition as Predictors of Obsessive-Compulsive Symptoms: A Prospective Study

A number of models of Obsessive Compulsive Disorder (OCD) stress the role of beliefs in the development of symptoms. However, they differ as to which beliefs they consider central. These beliefs fall into two categories—cognitive and metacognitive. The current study compared the relative contribution of cognition and metacognition as prospective predictors of obsessive-compulsive symptoms. We used measures of cognitive beliefs derived from cognitive theories of OCD (e.g., Salkovskis, 1985) a measure of metacognition derived from Wells' metacognitive model (Wells, A., 1997), and another metacognitive measure that draws from several models of OCD (e.g., Rachman, 1997). We controlled for worry and beliefs concerning overestimation of threat. Thought-fusion, a metacognitive belief implicated in Wells' model, emerged as an independent prospective predictor of O-C symptoms but other beliefs did not. The results add to a growing database supporting the metacognitive model.
Free-Space Characterization of the Permeability of Inhomogeneous Magneto-Dielectric Materials

A free-space methodology specifically designed for characterizing inhomogeneous magneto-dielectric materials is presented. The associated modeling is performed with the finite-element method combined with the Born linearized approximation even if the dielectric constants of the materials are known to be large. Due to the introduction of a metallic element, a decoupling of the magnetic and dielectric effects is encountered. This enables us to recover the magnetic characteristic of the material from measured scattered fields, thanks to the inversion of the linear model. The entire methodology is described herein and assessed thanks to an experimental validation.
Panel of computing students with disabilities

A panel of college students with disabilities who are computing majors or have taken multiple computing courses will describe their experiences both in and out of the classroom. The goal of the panel is to provide the audience with an opportunity to hear first-hand how their educational needs were met as non-traditional computing students. In addition to the panelists' short presentations, the moderator will facilitate a dialog between the members of the audience and the panelists.
Conceptual Modeling as a Toolbox for Grounded Theorists

Conceptual modeling is proposed as a set of analytic procedures that further the grounded theory approach to theory-discovery and development. The compatibility between grounded theory and conceptual modeling is discussed, and data from a short ethnographic study of a hair salon are used to illustrate the roles of conceptual modeling in the early stages of theory discovery. The major focus of conceptual modeling is on three simultaneous, explicit, continuing respecification dialogues: the nature and dimensionalization of concepts, the relative importance of concepts, and the nature of relationships among concepts. We argue that this focus facilitates the discovery and development of conceptually dense theories.
Adaptive noise dictionary design for noise robust exemplar matching of speech

This paper investigates an adaptive noise dictionary design approach to achieve an effective and computationally feasible noise modeling for the noise robust exemplar matching (N-REM) framework. N-REM approximates noisy speech segments as a linear combination of multiple length exemplars in a sparse representation (SR) formulation. Compared to the previous SR techniques with a single overcomplete dictionary, N-REM uses smaller dictionaries containing considerably fewer noise exemplars. Hence, the noise exemplars have to be selected with care to accurately model the spectrotem-poral content of the actual noise conditions. For this purpose, in a previous work, we introduced a noise exemplar selection stage before performing recognition which extracts noise exemplars from a few noise-only training sequences chosen for each target noisy utterance. In this work, we explore the impact of the several design parameters on the recognition accuracy by evaluating the system performance on the CHIME-2 and AURORA-2 databases.
Perseveration in Tool Use: A Window for Understanding the Dynamics of the Action-Selection Process

Two experiments investigated how 3-year-old children select a tool to perform a manual task, with a focus on their perseverative parameter choices for the various relationships involved in handling a tool: the actor-to-tool relation and the tool-to-target relation (topology). The first study concerned the parameter value for the tool-to-target relation by asking how children use a cane for either pushing an object further away (exclosure; outside the hook) or pulling an object nearby (enclosure; inside the hook). The second study concerned the parameter value for the hand-to-tool relation by assessing the hand used for grasping a spoon to feed a puppet. Results from both studies showed that on the first trial, choices were driven by task information. However, when the task switched from pulling to pushing or from left hand to right hand, or vice versa, children persevered with the choice they made during the 4 previous trials. Results are discussed in terms of the dynamical field modeling work of Esther Thelen and her colleagues. Our findings underscore Thelen's hypotheses that: (a) the action-selection process is a dynamic affair, affected by multiple influences at different time scales and its own intrinsic dynamics; and (b) that perseverative behavior is a general phenomenon that is neither indicative for a specific period in the development, nor for a particular task. Similarly, we argue that the presence (or absence) of causal understanding emerges from the action-selection process, rather than determining this process.
Fixing ally's growing pains with velocity modeling

Mapping the router topology is an important component of Internet measurement. Alias resolution, the process of mapping IP addresses to routers, is critical to accurate Internet mapping. Ally, a popular alias resolution tool, was developed to resolve aliases in individual ISPs, but its probabilistic accuracy and need to send O(n2) probes to infer aliases among n IP addresses make it unappealing for large-scale Internet mapping. In this paper, we present RadarGun, a tool that uses IP identifier velocity modeling to improve the accuracy and scalability of the Ally-based resolution technique. We provide analytical bounds on Ally's accuracy and validate our predicted aliases against Ally. Additionally, we show that velocity modeling requires only O(n) probes and thus scales to Internet-sized mapping efforts.
Proclaimed graduate attributes of Australian universities: patterns, problems and prospects

Purpose – Graduate attributes are about to be policed by the Tertiary Education Quality and Standards Agency (TEQSA) in Australia. All universities proclaim them on their public web sites. The aim of this paper is to determine whether distinct patterns or clusters are apparent in the declared graduate attributes declared by Australian universities on their web sites.Design/methodology/approach – Work by scholars in the field of graduate attribute building is discussed, with particular reference to the tension between disciplinarity and attribute building and the relative failure of techniques so far espoused to demonstrate student attainment of graduate attributes. Some promising approaches to the serious problems of building and demonstrating graduate attributes are captured, and some recommendations for addressing the urgent and serious issues confronting the sector are put forward.Findings – Graduate attributes of each university are publicly available and these can be related to discussions of employe.
Real-Time Community Detection in Large Social Networks on a Laptop

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.