Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.
Surface techniques for vortex visualization

This paper presents powerful surface based techniques for the analysis of complex flow fields resulting from CFD simulations. Emphasis is put on the examination of vortical structures. An improved method for stream surface computation that delivers accurate results in regions of intricate flow is presented, along with a novel method to determine boundary surfaces of vortex cores. A number of surface techniques are presented that aid in understanding the flow behavior displayed by these surfaces. Furthermore, a scheme for phenomenological extraction of vortex core lines using stream surfaces is discussed and its accuracy is compared to one of the most established standard techniques.
Impact of uremia, diabetes, and peritoneal dialysis itself on the pathogenesis of peritoneal sclerosis: a quantitative study of peritoneal membrane morphology.

BACKGROUND AND OBJECTIVES Peritoneal interstitial fibrosis and hyalinizing vasculopathy were induced by peritoneal dialysis and other associated conditions (e.g., uremia). A quantitative method for peritoneal biopsy evaluation is required to investigate possible causative factors and severity of the peritoneal dialysis-related peritoneal alterations. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Peritoneal biopsy specimens from 173 uremic (before peritoneal dialysis) and 80 peritoneal dialysis patients with or without impaired ultrafiltration capacity were evaluated by average peritoneal thickness of submesothelial compact zone measured at five randomly selected points of peritoneum and by lumen/vessel diameter ratio at postcapillary venule. RESULTS The average peritoneal thickness was increased in uremic patients and progressively thickened as the duration of peritoneal dialysis prolonged. The lumen/vessel diameter ratio was lower in uremia than normal and progressively decreased as the duration of peritoneal dialysis prolonged. In pre-peritoneal dialysis peritoneum, patients with diabetes showed significant decrease in lumen/vessel diameter ratio compared with patients without diabetes. The average peritoneal thickness was significantly higher in patients with impaired ultrafiltration capacity than in patients with maintained ultrafiltration capacity; however, no significant difference was observed in the postcapillary venule thickness and lumen/vessel diameter ratio between the two groups. CONCLUSIONS The average peritoneal thickness and lumen/vessel diameter ratio were useful morphologic parameters to quantify the severity of the peritoneal alterations in uremic and peritoneal dialysis patients. Uremia and diabetes had an impact on the pathogenesis of peritoneal sclerosis in pre-peritoneal dialysis peritoneum. Peritoneal dialysis treatment itself had a much stronger impact on the progression of peritoneal sclerosis.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic, and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing (NGS) data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge.net/projects/tlex/. Abbreviations TE transposable element NGS next-generation sequencing LTR long-terminal repeat TSD target site duplication PTS putative target site PE paired-end
Gingival crevicular fluid periostin levels in chronic periodontitis patients following nonsurgical periodontal treatment with low-level laser therapy

Objective: Periostin is a matricellular protein highly expressed in periosteum, periodontal ligament and is essential for tissue integrity and maturation. It plays a role in collagen fibrillogenesis and is downregulated in periodontal disease. Biostimulation utilizing low-level laser therapy (LLLT) influences periodontal ligament fibroblast proliferation. This study was conducted with the objective of estimating periostin levels in chronic periodontitis (CP) patients following LLLT as an adjunct to root surface debridement (RSD). Materials and Methods: Thirty periodontally healthy participants (Group I) and sixty CP participants were recruited. Based on the therapeutic intervention, CP patients were allocated to either RSD (Group II) or to RSD with LLLT (Group III) group. Clinical parameters and gingival crevicular fluid (GCF) periostin levels were assessed at the baseline and at the 3rd month. Results: Periostin levels were significantly lower in CP patients when compared to healthy individuals at the baseline (P < 0.01). Following nonsurgical periodontal treatment (NSPT), periostin levels significantly increased in both Group II and III, when compared to baseline values (P < 0.001). Comparison of mean periostin levels between both the treatment groups showed a significant increase in LLLT group than RSD at the 3rd month (P < 0.05). Conclusion: Within the limitations of the present study, LLLT application was found to have additional benefits over RSD with respect to clinical periodontal parameters and GCF periostin levels. Moreover, periostin may be used as a possible biomarker to evaluate the outcome following NSPT.
Rheology of poly (lactic acid)-based systems

Abstract Being commercialized in 1992, poly (lactic acid) (PLA) has been considered for biomedical applications and as a reliable substitute for a wide range of commodity and engineering applications where noncompostable petroleum-based polymers are currently being used. However, PLA suffers from series of drawbacks and it would not be applicable unless these shortcomings resolve somewhat. Besides the PLA’s brittleness and low toughness which originate from its higher glass transition temperature, the major shortcomings which negatively influence the other features of PLA are its low melt strength and slow crystallization kinetics. These weaknesses limit the processability, formability and foamability of PLA, and hence, the manufacturing of PLA based products. In this context, the improvement of rheological and viscoelastic properties of PLA is of a great importance as it enhances the melt strength. To control the PLA’s rheological and viscoelastic properties, various attempts such as varying the D-lactide content in PLA molecules, increasing the PLA’s molecular weight, the use of chain extender and branching, controlling the PLA’s crystallization, compounding with micro-/nano-sized fillers and blending with other polymers have been considered. This article critically reviews these studies that have been conducted so far on rheological investigations of various PLA-based systems.
Homologous Basal Ganglia Network Models in Physiological and Parkinsonian Conditions

The classical model of basal ganglia has been refined in recent years with discoveries of subpopulations within a nucleus and previously unknown projections. One such discovery is the presence of subpopulations of arkypallidal and prototypical neurons in external globus pallidus, which was previously considered to be a primarily homogeneous nucleus. Developing a computational model of these multiple interconnected nuclei is challenging, because the strengths of the connections are largely unknown. We therefore use a genetic algorithm to search for the unknown connectivity parameters in a firing rate model. We apply a binary cost function derived from empirical firing rate and phase relationship data for the physiological and Parkinsonian conditions. Our approach generates ensembles of over 1,000 configurations, or homologies, for each condition, with broad distributions for many of the parameter values and overlap between the two conditions. However, the resulting effective weights of connections from or to prototypical and arkypallidal neurons are consistent with the experimental data. We investigate the significance of the weight variability by manipulating the parameters individually and cumulatively, and conclude that the correlation observed between the parameters is necessary for generating the dynamics of the two conditions. We then investigate the response of the networks to a transient cortical stimulus, and demonstrate that networks classified as physiological effectively suppress activity in the internal globus pallidus, and are not susceptible to oscillations, whereas parkinsonian networks show the opposite tendency. Thus, we conclude that the rates and phase relationships observed in the globus pallidus are predictive of experimentally observed higher level dynamical features of the physiological and parkinsonian basal ganglia, and that the multiplicity of solutions generated by our method may well be indicative of a natural diversity in basal ganglia networks. We propose that our approach of generating and analyzing an ensemble of multiple solutions to an underdetermined network model provides greater confidence in its predictions than those derived from a unique solution, and that projecting such homologous networks on a lower dimensional space of sensibly chosen dynamical features gives a better chance than a purely structural analysis at understanding complex pathologies such as Parkinson's disease.
Transfer Learning in Collaborative Filtering for Sparsity Reduction Via Feature Tags Learning Model

Recently, many scholars have proposed recommendation models to alleviate the sparsity problem by transferring rating matrix in other domains. But different domains have different rating scales. Simple process for the rating scale does not reflect the real situation. The diversity of rating scales may cause the opposite effect, making the recommendation results more imprecise. In this paper, we propose a feature tags learning model which learning the common feature tags from other domain. This model ignores the difference of rating scales between two domains, and focus on studying the feature tags. Using its own rating values to fill the missing value. We perform extensive experiments to show that our proposed model outperforms the state-of-the-art CF methods for the cross-domain recommendation task.
SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images

Motivation: Microarray profiling of mRNA abundance is often ill suited for temporal–spatial analysis of gene expressions in multicellular organisms such as Drosophila. Recent progress in image-based genome-scale profiling of whole-body mRNA patterns via in situ hybridization (ISH) calls for development of accurate and automatic image analysis systems to facilitate efficient mining of complex temporal–spatial mRNA patterns, which will be essential for functional genomics and network inference in higher organisms. Results: We present SPEX2, an automatic system for embryonic ISH image processing, which can extract, transform, compare, classify and cluster spatial gene expression patterns in Drosophila embryos. Our pipeline for gene expression pattern extraction outputs the precise spatial locations and strengths of the gene expression. We performed experiments on the largest publicly available collection of Drosophila ISH images, and show that our method achieves excellent performance in automatic image annotation, and also finds clusters that are significantly enriched, both for gene ontology functional annotations, and for annotation terms from a controlled vocabulary used by human curators to describe these images. Availability: Software will be available at http://www.sailing. cs.cmu. edu/ Contact: epxing@cs.cmu. edu Supplementary information: Supplementary data are avilable at Bioinformatics online.
Stability analysis for delay differential equations with multidelays and numerical examples

In this paper we are concerned with the asymptotic stability of the delay differential equation x'(t) = A 0 x(t) + A k x(tτ k ), where A 0 , A k ∈ C d×d are constant complex matrices, and x(tτ k ) = (x 1 (t - τ k1 ),x 2 (t - τ k2 ),. , x d (t - τ kd )) T ,τ kl > 0 stand for n x d constant delays (k = 1,.,n, I = 1,.,d). We obtain two criteria for stability through the evaluation of a harmonic function on the boundary of a certain region. We also get similar results for the neutral delay differential equation x'(t) = Lx(t) + M i x(t - τ i ) + N j x'(t - τ' j ), where L, M i , and Nj e C d×d are constant complex matrices and τ i ,τ' j > 0 stands for constant delays (i = 1,.,m, j = 1,.,n). Numerical examples on various circumstances are shown to check our results which are more general than those already reported.
Lessons Learned: The Role of the Classics at Black Colleges and Universities

Abstract:This article applies the paradigm of Black insurgency and social uplift to the teaching of the Greek and Latin classics at Black colleges and universities during the late 19th and early 20th centuries. It demonstrates how study of the classics helped construct the tools of Black agency by imparting three important lessons: the knowledge that African Americans were indeed linked to the classical civilizations through northern Africa, which therefore gave them the inherent right to study the classics; the development of leadership training, particularly through study of the classical rhetoricians; and a variety of techniques of resistance, ranging from dissimulation to overt acts of physical resistance. The authors use three case examples: Howe Institute in Memphis, Tennessee; the J. K. Brick Industrial School in Enfield, North Carolina; and the Florida Agricultural and Mechanical College.
Automatically Labeling Semantic Classes

Systems that automatically discover semantic classes have emerged in part to address the limitations of broad-coverage lexical resources such as WordNet and Cyc. The current state of the art discovers many semantic classes but fails to label their concepts. We propose an algorithm labeling semantic classes and for leveraging them to extract is-a relationships using a top-down approach.
Fast Multiple Access Selection through variable power transmissions

Many wireless applications demand a fast mechanism to detect the packet from a node with the highest priority (ldquobest noderdquo) only, while packets from nodes with lower priority are irrelevant. In this paper, we introduce an extremely fast contention-based multiple access algorithm that selects the best node and requires only local information of the priorities of the nodes. The algorithm, which we call variable power multiple access selection (VP-MAS), uses the local channel state information from the accessing nodes to the receiver, and maps the priorities onto the receive power. It is based on a key result that shows that mapping onto a set of discrete receive power levels is optimal, when the power levels are chosen to exploit packet capture that inherently occurs in a wireless physical layer. The VP-MAS algorithm adjusts the expected number of users that contend in each step and their respective transmission powers, depending on whether previous transmission attempts resulted in capture, idle channel, or collision. We also show how reliable information regarding the total received power at the receiver can be used to improve the algorithm by enhancing the feedback mechanism. The algorithm detects the packet from the best node in 1.5 to 2.1 slots, which is considerably lower than the 2.43 slot average achieved by the best algorithm known to date.
The Immunoglobulin A Antibody Response in Clinical Subsets of Mucous Membrane Pemphigoid

Background: Mucous membrane pemphigoid (MMP) is an immunobullous disease. In MMP there is frequently a mixed antibody response with the presence of IgA and/or IgG antibodies directed toward basement membrane zone antigens. The IgG antibody response in MMP has been studied, but the antigens to which the IgA antibodies react have not been studied. Objective: To determine the IgA autoantibody reactivity profiles in patients with MMP. Methods: Patients who had both ocular and oral MMP were compared with patients who had ocular or oral MMP and with patients who had cutaneous linear IgA disease (LABD) by Western immunoblot studies. Results: Five of 15 MMP patients and 1 of 5 LABD patients had IgA antibodies reactive with the 180-kD bullous pemphigoid antigen. Seven of 15 MMP patients had IgA antibodies reactive with the 97-kD LABD antigen. Conclusion: Major antigens in IgA MMP are the 180-kD bullous pemphigoid antigen and the 97-kD LABD antigen.
Semi-Supervised Structured Output Learning Based on a Hybrid Generative and Discriminative Approach

This paper proposes a framework for semi-supervised structured output learning (SOL), specifically for sequence labeling, based on a hybrid generative and discriminative approach. We define the objective function of our hybrid model, which is written in log-linear form, by discriminatively combining discriminative structured predictor(s) with generative model(s) that incorporate unlabeled data. Then, unlabeled data is used in a generative manner to increase the sum of the discriminant functions for all outputs during the parameter estimation. Experiments on named entity recognition (CoNLL-2003) and syntactic chunking (CoNLL-2000) data show that our hybrid model significantly outperforms the stateof-the-art performance obtained with supervised SOL methods, such as conditional random fields (CRFs).
A Space Reuse Strategy for Flash Translation Layers in SLC NAND Flash Memory Storage Systems

This paper presents a space reuse strategy for flash translation layers in SLC nand flash storage systems. The basic idea is to prevent a block with many free pages from being erased in a merge operation. The preserved blocks are further reused as replacement blocks. In such a way, the space utilization and the number of erase counts of each block in a nand flash are enhanced. By employing the reuse strategy, we propose a reuse-aware flash translation layer (FTL) called reuse-aware NFTL (RNFTL) to improve the endurance and space utilization of single level cell (SLC) nand flash. We provide the performance analysis of RNFTL for frequent update operations and sequential write operations, and theoretically compare RNFTL with representative FTL schemes. We also discuss the opportunity to apply the reuse strategy in log-block-based FTL schemes. To the best of our knowledge, this is the first work to employ a space reuse strategy in FTLs to improve the space utilization and endurance of nand flash. The experiments have been conducted on a set of traces collected from real workload in daily life. The results show that the space reuse strategy can effectively improve space utilization, block lifetime and wear-leveling compared with the previous work.
Loving and Loathing Physical Education: An Exploration of Students’ Beliefs

This article describes a recent study that investigated the physical education (PE) beliefs of a particular population of students (i.e., female and male students in Grades 4 through 10 from a single school stream). Through their completion of an adapted survey, students (N = 506) were able to share their PE beliefs in relation to five separate subscales: PE Interest, PE Status, PE Connotations, PE Teachers, and PE Curriculum. Results suggest that grade and gender differences exist with respect to these subscales. Consequently, it is herein suggested that the discovery of such differences within this case study merits considerations for educational change, as well as continued and deeper inquiries into understanding the nature of PE beliefs for female and male students in various grade levels. Cet article décrit une étude récente qui a porté sur les croyances qu'a une population particulière d'élèves (c.-à-d. filles et garçons, de la 4e à la 10e année, d'une école à voie unique) par rapport à l'éducation physique. Par le biais d'une enquête adaptée, les élèves (N = 506) ont partagé leurs croyances sur l'éducation physique en fonction de cinq sous-échelles séparées: intérêt, statut, sens affectifs, enseignants et curriculum. Les résultats donnent à penser qu'il existe, par rapport à ces sous-échelles, des différences liées à l'année scolaire et au genre. On propose donc que les différences révélées par cette étude de cas méritent d'être considérées dans le contexte de changements pédagogiques et d'être étudiées en profondeur et à long terme pour comprendre la nature des croyances d'élèves, filles et garçons et à divers années scolaires, relatives à l'éducation physique.
CD49f‐Positive Testicular Cells in Saanen Dairy Goat Were Identified as Spermatogonia‐Like Cells by miRNA Profiling Analysis

miRNAs, a type of small RNA, play critical roles in mammalian spermatogenesis. Spermatogonia are the foundation of spermatogenesis and are valuable for the study of spermatogenesis. However, the expression profiling of the miRNAs in spermatogonia of dairy goats remains unclear. CD49f has been one of the surface markers used for spermatogonia enrichment by magnetic activated cell sorting (MACS). Therefore, we used a CD49f microbead antibody to purify CD49f‐positive and ‐negative cells of dairy goat testicular cells by MACS and then analysed the miRNA expression in these cells in depth using Illumina sequencing technology. The results of miRNA expression profiling in purified CD49f‐positive and ‐negative testicular cells showed that 933 miRNAs were upregulated in CD49f‐positive cells and 916 miRNAs were upregulated in CD49f‐negative cells with a twofold increase, respectively; several miRNAs and marker genes specific for spermatogonial stem cells (SSCs) in testis had a higher expression level in CD49f‐positive testicular cells, including miR‐221, miR‐23a, miR‐29b, miR‐24, miR‐29a, miR‐199b, miR‐199a, miR‐27a, and miR‐21 and CD90, Gfra1, and Plzf. The bioinformatics analysis of differently expressed miRNAs indicated that the target genes of these miRNAs in CD49f‐positive cells were involved in cell‐cycle biological processes and the cell‐cycle KEGG pathway. In conclusion, our comparative miRNAome data provide useful miRNA profiling data of dairy goat spermatogonia cells and suggest that CD49f could be used to enrich dairy goat spermatogonia‐like cells, including SSCs. J. Cell. Biochem. 115: 1712–1723, 2014. © 2014 Wiley Periodicals, Inc.