Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro neural/glial differentiation potential of periodontal ligament stem cells

Introduction It is known that periodontal ligament stem cells (PDLSCs) can differentiate into cementoblast-like cells, adipocytes and collagen-forming cells. However, whether PDLSCs are able to differentiate into Schwann cells and which method is best for their neural induction remain unknown. We attempted to determine whether PDLSCs possessed the potential for neural differentiation in vitro. Materials and methods We isolated and multiplied PDLSCs from periodontal ligaments obtained from the teeth (n = 24) of 8-month-old beagle dogs. Four protocols with different chemicals and growth factors were adopted to induce the PDLSCs to differentiate into Schwann cells. Immunochemistry, RT-PCR and qRT-PCR were performed to investigate the in vitro neural differentiation potential of PDLSCs. Results We compared the 4 different protocols and showed that all 4 protocols could successfully induce PDLSCs to express nestin, GFAP and S100, markers for Schwann cells. Further, qRT-PCR revealed relative differences in the expression levels of these 3 genes in differentiated PDLSCs obtained by different protocols. Conclusions We conclude that PDLSCs have neural/glial differentiation potential in vitro and that neural/glial differentiation can be induced in PDLSCs if suitable protocols are followed. We also found that supplementing the growth medium with suitable growth factors is more effective than applying chemicals alone. While nerve growth factor is more effective than platelet-derived growth factor for inducing neural/glial differentiation in PDLSCs, pre-induction of PDLSCs with dimethyl sulphoxide yields better results than those obtained with all-trans-retinoic acid.
Spectral knowledge database for sugarcane identification with multi-temporal remote sensing images

Multi-temporal remote sensing data can provide much more information that could be used to improve the accuracy of classification of vegetation types. However, it is always required to manually select a set of training samples by using conventional supervised classification methods, which is a time-consuming and costly task. In this paper, a new classification method based on spectral knowledge database (SKD) has been proposed. The spectral knowledge database is composed by a serious of spectral datasets, prior knowledge, and remote sensing models. For a specific remote sensing image, the data of object class can be simulated based on the knowledge database, which can be used to generate the classification rules. With this approach, an experiment of sugarcane identification was conducted. And the results show that the accuracy of the results by using proposed method was comparable to that by using supervised classification.
Stoichiometry of the Photosynthetic Apparatus and Phycobilisome Structure of the Cyanobacterium Plectonema boryanum UTEX 485 Are Regulated by Both Light and Temperature1

The role of growth temperature and growth irradiance on the regulation of the stoichiometry and function of the photosynthetic apparatus was examined in the cyanobacterium Plectonema boryanum UTEX 485 by comparing mid-log phase cultures grown at either 29°C/150 μmol m−2 s−1, 29°C/750 μmol m−2 s−1, 15°C/150 μmol m−2 s−1, or 15°C/10 μmol m−2s−1. Cultures grown at 29°C/750 μmol m−2s−1 were structurally and functionally similar to those grown at 15°C/150 μmol m−2 s−1, whereas cultures grown at 29°C/150 μmol m−2 s−1were structurally and functionally similar to those grown at 15°C/10 μmol m−2 s−1. The stoichiometry of specific components of the photosynthetic apparatus, such as the ratio of photosystem (PS) I to PSII, phycobilisome size and the relative abundance of the cytochrome b6/f complex, the plastoquinone pool size, and the NAD(P)H dehydrogenase complex were regulated by both growth temperature and growth irradiance in a similar manner. This indicates that temperature and irradiance may share a common sensing/signaling pathway to regulate the stoichiometry and function of the photosynthetic apparatus in P. boryanum. In contrast, the accumulation of neither the D1 polypeptide of PSII, the large subunit of Rubisco, nor the CF1 α-subunit appeared to be regulated by the same mechanism. Measurements of P700 photooxidation in vivo in the presence and absence of inhibitors of photosynthetic electron transport coupled with immunoblots of the NAD(P)H dehydrogenase complex in cells grown at either 29°C/750 μmol m−2 s−1 or 15°C/150 μmol m−2 s−1 are consistent with an increased flow of respiratory electrons into the photosynthetic intersystem electron transport chain maintaining P700 in a reduced state relative to cells grown at either 29°C/150 μmol m−2 s−1 or 15°C/10 μmol m−2 s−1. These results are discussed in terms of acclimation to excitation pressure imposed by either low growth temperature or high growth irradiance.
Residential proximity to major roadways is associated with increased prevalence of allergic respiratory symptoms in children.

INTRODUCTION AND OBJECTIVE Numerous epidemiologic studies have reported increased risk of allergic rhinitis and asthma in relation to 'western life-style', which represents diversity of factors. We hypothesized that residential proximity to major roadways, reflecting an exposure to traffic-related air pollution, is associated with prevalence of allergic respiratory symptoms in children. MATERIALS AND METHODS A total of 8290 individuals of two age groups: 16 year olds and 7 year olds from Krakow, Poland were included. We used the Polish version of the International Study of Asthma and Allergy in Childhood supplemented with a question concerning the distance between a responder's house and a high traffic density road: below 200 m, from 200-500 m, or more than 500 m. RESULTS Children and adolescents with a residential proximity closer to a major roadway had more frequent asthma-related symptoms in the last 12 months and at any time in the past. Consistent with the increased frequency of asthmatic symptoms, responders residing within 200 meters complained more often of sneezing, runny or blocked nose accompanied by itchy-watery eyes and hay fever in comparison to responders who resided 200-500 meters from a major roadway. The lowest rate of nasal symptoms was observed in residents living in the distance to major roads (> 500 meters). The rate of positive answers decreased in a distant-dependent manner. CONCLUSIONS Our findings suggest an important spatial relationship between the distance from a major roadway and the evaluated respiratory symptoms. The results emphasize the need for more comprehensive air quality policies within urban areas with increased motor vehicle density.
Embedding undergraduate research experiences within the curriculum: a cross-disciplinary study of the key characteristics guiding implementation

Undergraduate research experiences provide students with opportunities to engage in high-impact experiential learning. Although prevalent in the sciences, there are now extensive banks of case studies demonstrating the use of undergraduate research as an educationally enriching activity across many disciplines. This study investigated the diversity of undergraduate research opportunities available across a wide range of disciplines at a large, research-intensive, Australian university. Through extensive interviews, 68 undergraduate research programmes across 26 discipline-based schools were characterised. A typology of undergraduate research models is proposed, revealing key characteristics underlying the ways in which research experiences are embedded in undergraduate curricula across a diverse range of disciplinary contexts. This provides guidance to academics, administrators and policymakers seeking to improve student access to undergraduate research experiences.
The Zebrafish fade out mutant: a novel genetic model for Hermansky-Pudlak syndrome.

PURPOSE To characterize retinal morphology and visual system function in the zebrafish mutant fade out (fad) and to establish the mutant as a lower vertebrate model for Hermansky-Pudlak syndrome (HPS). METHODS Retinal morphology of fad larvae was examined between 3 and 9 days postfertilization (dpf) by standard histology, transmission electron microscopy, and immunohistochemistry examination. Apoptotic cells were visualized by TdT-mediated dUTP nick-end labeling (TUNEL) staining. Visual system function was probed by electroretinography and behavioral assessment by optokinetic response measurements. Blood clotting was evaluated by time to occlusion testing of blood vessels as an arterial thrombosis assay. The chromosomal location of fad was determined by simple sequence-length polymorphism mapping. Genomic fragments of candidate genes were cloned by standard molecular techniques and mapped to the zebrafish genome by radiation hybrid mapping. RESULTS Mutant fad larvae are hypopigmented and show structural defects in the outer retina. Melanosomes of these larvae in the retinal pigment epithelium are hypopigmented, generally smaller, and progressively reduced in number compared to nonmutant larvae. Progressive microvilli protrusions into the photoreceptor cell layer are not detectable, and photoreceptor outer segments get shorter and are misaligned. Photoreceptors subsequently undergo apoptosis, with a peak of cell death at 6 dpf. Electrical responses of the retina and visual performance are severely reduced. Blood clotting is prolonged in mutant fad larvae. Genomic mapping of fad reveals distinct genomic positions of the mutant gene from known human HPS genes. CONCLUSIONS The fad mutant shows syndromic defects in pigmentation, outer retinal structure and function, and blood clotting. This syndrome is characteristic of Hermansky-Pudlak syndrome (HPS), making fad a novel genetic model of HPS. The gene does not cosegregate with the known human HPS genes, suggesting a novel molecular cause of HPS.
Building shared trees using a one-to-many joining mechanism

This paper presents a new approach for building shared trees which have the capability of providing multiple routes from the joining node onto an existing tree. The approach follows a design parameter of CBT and PIM in that it operates independently of any unicast routing protocol. However, a paradigm shift is introduced such that trees are built in an on-demand basis through the use of a one-to-many joining mechanism. In addition, the paper presents optimisations of the new mechanism to help constrain its impact in the case where many receivers exist for a given multicast group.
Prevention, diagnosis and treatment of high‐throughput sequencing data pathologies

High‐throughput sequencing (HTS) technologies generate millions of sequence reads from DNA/RNA molecules rapidly and cost‐effectively, enabling single investigator laboratories to address a variety of ‘omics’ questions in nonmodel organisms, fundamentally changing the way genomic approaches are used to advance biological research. One major challenge posed by HTS is the complexity and difficulty of data quality control (QC). While QC issues associated with sample isolation, library preparation and sequencing are well known and protocols for their handling are widely available, the QC of the actual sequence reads generated by HTS is often overlooked. HTS‐generated sequence reads can contain various errors, biases and artefacts whose identification and amelioration can greatly impact subsequent data analysis. However, a systematic survey on QC procedures for HTS data is still lacking. In this review, we begin by presenting standard ‘health check‐up’ QC procedures recommended for HTS data sets and establishing what ‘healthy’ HTS data look like. We next proceed by classifying errors, biases and artefacts present in HTS data into three major types of ‘pathologies’, discussing their causes and symptoms and illustrating with examples their diagnosis and impact on downstream analyses. We conclude this review by offering examples of successful ‘treatment’ protocols and recommendations on standard practices and treatment options. Notwithstanding the speed with which HTS technologies – and consequently their pathologies – change, we argue that careful QC of HTS data is an important – yet often neglected – aspect of their application in molecular ecology, and lay the groundwork for developing a HTS data QC ‘best practices’ guide.
Enhancing downbeat detection when facing different music styles

This paper focuses on the automatic rhythm analysis of musical audio at the bar level. We propose a novel approach for robust downbeat detection. It uses well-chosen complementary features, inspired by musical considerations. In particular, a note accentuation model and a detection of pattern changes are introduced. We estimate the time signature by examining the similarity of frames at the beat level. The features are selected through a linear SVM model or a weighted sum. The whole system is evaluated on five different datasets of various musical styles and shows improvement over the state of the art.
Capsid Is a Dominant Determinant of Retrovirus Infectivity in Nondividing Cells

ABSTRACT A major difference between lentiviruses such as human immunodeficiency virus (HIV) and most other retroviruses is their ability to productively infect nondividing cells. We present here genetic evidence for involvement of the capsid protein (CA) in the infectious phenotype in nondividing cells. A chimeric HIV type 1 (HIV-1) in which the MA and CA of HIV-1 are replaced with the MA, p12, and CA encoding sequences from murine leukemia virus (MLV) loses the ability to efficiently infect nondividing cells. Analysis of the accumulation of two-long-terminal-repeat circles implies that the impairment of nuclear transport of preintegration complexes is responsible for the restricted infection of this chimeric virus in nondividing cells. Incorporation of MLV MA and MLV p12 into HIV virions alone does not exert any adverse effects on viral infection in interphase cells. These results suggest that CA is the dominant determinant for the difference between HIV and MLV in the ability to transduce nondividing cells.
To Quote or not to Quote: Citation Strategies in the Encyclopédie

Ever since the first volume of the Encyclopédie was published in 1751, critics have complained about its liberal borrowings from other sources. This article explores some of the reasons why not citing other sources may have been an important publishing and philosophical strategy. Using a data-mining program that automatically flags likely matches between texts, we were able to identify thousands of citations and to discover clear citational patterns. Taking into account the complicated system of publishing permissions in Old Regime France, we show that many instances of non-citation occurred for books that were published anonymously and/or without a royal privilège. Accordingly, we argue that there was a “subversive style” of non-citation: by not identifying their references, contributors were able to incorporate into the Encyclopédie extensive passages of banned or forbidden books.
QUAASY: QUality Assurance of Adaptive SYstems

The emerging approach to tackle the increasing complexity of today's software systems is the use of self-adaptation techniques. Modeling and implementing adaptivity features is a burdensome and error-prone task that potentially results in erroneous system models. As a consequence, quality analysis and assurance must be considered early in the development of self-adaptive systems. We propose a quality assurance approach for self-adaptive systems in terms of an integrated modeling and analysis approach, which helps identifying errors in modeled self-adaptive systems early in the design process. We employ a modeling language for self-adaptive systems including adaptation rules and formally define their semantics. Given the language and its formal semantics, we formulate quality properties, such as fairness of the specified adaptation rule system. These quality properties are verified using a model checking approach.
Analysis of cardiac pacemaker potential using a "voltage clamp" technique.

VASSALEE, MARIO. Analysis of card& pacemaker potential using a %ltage clamf3 technique. Am. J. Physiol. 210(6): 1335-1341. I g66. -Diastolic depolarization was studied by means of ccvoItage clamp” technique in short mammalian Purkinje fibers. Clamping the membrane potential at the maximal diastolic value resulted in an inward current rising with a time constant of 3 set in 5.4 mM K, indicating that slow depolarization is essentially a time-dependent process. Membrane slope resistance during clamp increased as a function of time, suggesting a decrease in potassium conductance rather than an increase in sodium conductance. Clamping the membrane to the calculated potassium equilibrium potential resulted in a steady inward current; at more negative clamps the inward current decreased with time. The latter findings were obtained also in sodium-free solution, indicating that a fall in the activity of an electrogenic sodium pump does not play a major role in the diastolic depolarization process. Diastolic depolarization can be initiated at any time during the plateau by clamping to the maximal diastolic potential. The threshold for all-or-nothing repolarization was determined during the plateau and found to follow the expected time course.
i‐Patch: Interprotein contact prediction using local network information

Biological processes are commonly controlled by precise protein‐protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i‐Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i‐Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i‐Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i‐Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i‐Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Compiling with continuations, continued

We present a series of CPS-based intermediate languages suitable for functional language compilation, arguing that they have practical benefits over direct-style languages based on A-normal form (ANF) or monads. Inlining of functions demonstrates the benefits most clearly: in ANF-based languages, inlining involves a re-normalization step that rearranges let expressions and possibly introduces a new 'join point' function, and in monadic languages, commuting conversions must be applied; in contrast, inlining in our CPS language is a simple substitution of variables for variables. We present a contification transformation implemented by simple rewrites on the intermediate language. Exceptions are modelled using so-called 'double-barrelled' CPS. Subtyping on exception constructors then gives a very straightforward effect analysis for exceptions. We also show how a graph-based representation of CPS terms can be implemented extremely efficiently, with linear-time term simplification.
Ginkgo biloba in the treatment of sexual dysfunction due to antidepressant drugs

and the etiology of neuroleptic malignant syndrome. American Journal of Psychiatry, 156, 169±180. Meltzer, H. Y. and Fatemi, S. H. (1998). Treatment of schizophrenia. In The American Psychiatric Press Textbook of Psychopharmacology, 2nd edition, Schatzberg, A. F. and Nemero, C. B. (Eds), American Psychiatric Press, Washington, DC, pp. 747±774. Owens, M. J. and Simpson, G. M. (1998). Atypical antipsychotics. In The American Psychiatric Press Textbook of Psychopharmacology, 2nd edition, Schatzberg, A. F. and Nemero, C. B. (Eds), American Psychiatric Press, Washington, DC, pp. 323±348. Sachdev, P., Kruk, J., Kneebone, M. and Kissane, D. (1995). Clozapine-induced neuroleptic malignant syndrome: review and report of new cases. Journal of Clinical Psychopharmacology, 15, 365±371.
Principles of Linguistic Philosophy

The view of linguistic philosophy presented in Waismann's book is one which has become stock in trade of some analytic philosophers. Philosophical problems are engendered by a superficial view of language. We are misled by linguistic analogies. Because a word is used in one context with one meaning, we think that it can be used in all contexts in this way (pp. 11, 60, 78, 179). Consequently, Waismann conceives philosophical activity as not answering ‘deep’ questions, but rather as clarifying the misconceptions which drive us to ask such questions.
Failure is not an Option: Parental Expectations of Nigerian Voluntary Immigrants to the United States

The purpose of this study was to explore the socio-cultural and educational contexts of parental expectations of Nigerian voluntary immigrants to the United States. Immigrant or voluntary minorities are people who have migrated essentially of their own volition to the United States, or any other nation, because they seek more economic mobility, or a better life in general, and/or political freedom (Ogbu, 1995). This case study sought an explanation for the success in education attributed to these new African immigrants and their children. This study investigated the relationship among three factors: (a) parental expectations, (b) socio-cultural experiences, and (c) (adult) children’s internalization of their parent’s aspirations for them. The method of inquiry included phenomenological analysis on data collected through participants’ topical life-histories (Giorgio, 1985). The results of the study represent the Nigerian immigrants’ worldviews: a folk theory shared by their cultural and life experiences. The common threads running throughout their responses are ‘education is the number one priority,’ ‘hard work,’ ‘effort begets luck,’ and ‘failure is not an option. ’ Nigerian culture had a strong influence on the upbringing and fulfillment of expectations for the children of the participants.
Wikipedia Article Content Based Query Expansion in IR4QA System

This paper describes the work of our WUST group in NTCIR-8 on the subtask of English to Simplified Chinese and Simplified Chinese to Simplified Chinese information retrieval for question answering (EN-CS and CS-CS IR4QA). In order to enhance the precision and efficiency in question analysis, we employ a special question analysis method extracting more appropriate key terms and apply the query expansion technique gaining more relevant key terms based on Wikipedia article content related to the query.
Research Note: The Hidden Trade-offs of Cooperative Work — An Empirical Study

There is an increasing interest in introducing autonomous (or at least semi-autonomous) working groups into firms. The underlying view of 'cooperative work' is rather euphoric and uncritical. The aim of this research note, therefore, is to confront the often cited advantages for employees with an empirical study of an 'ideal' case. The presented group is ideal in that it features maximal autonomy of the group and maximal involvement of the group members in all the relevant decisions. The results of this investigation are extrapolated for 'normal' working groups in firms. In other words, the aspect examined is that group work may be less beneficial for employees than is often suggested by proponents of group work.