Miracle-dz/UniFAR-FTUs huggingface dataset:
Golgi positioning during cell migration

Andrea C. Uetrecht Golgi positioning during cell migration (Under the direction of Dr. Investigation of crucial aspects of cellular function in live cells frequently requires the loss of expression of a specific protein to gain insight into its function. It is also beneficial to combine this with either the enforced re-expression of a tagged version of the protein of interest to validate the phenotype, or the expression of fluorescently tagged marker proteins to investigate a particular phenomenon. Modifications to a short hairpin RNA-mediated knock-down lenti-viral delivery system described here enable the simultaneous expression of short hairpin RNA and a fluorescently-tagged rescue or marker protein to investigate specific cellular processes. The knock-down phenotype of capping protein ß was rescued by the simultaneous expression of a fluorescently tagged knock-down resistant version. Chromophore-assisted laser inactivation of capping protein ß demonstrated the acute loss of function phenotype and highlighted the necessity of loss of endogenous protein expression for the effects to be observed. Another modification in the lenti-viral vector system was used to demonstrate a role for coronin 1B in modulating the rate of actin retrograde flow. A final modification to the lenti-viral iii system enabled the simultaneous expression of two different fluorescent markers. This was used to investigate Golgi and nucleus positioning during migration. In Rat2 cells at the edge of an artificial wound, the Golgi and centrosome were positioned coincident to one another and were polarized to the front of the nucleus relative to the wound edge. Freely migrating cells expressing fluorescent markers of the Golgi and nucleus did not exhibit such polarity. Instead, Golgi positioning remained fairly constant relative to the nucleus independent of the direction of migration. Nucleus and Golgi positioning relative to the direction of migration was also independent of the speed or directional persistence. Lamellipodial dynamics such as the distance, duration or rate of protrusion were not substantially different along the nuclear-Golgi axis relative to other areas of the cell periphery. Together these data suggest that Golgi positioning in freely migrating cells is independent of the events at the periphery of the cell that are involved in migration. iv Fortune Cookie: The shortest distance between two points is no fun v ACKNOWLEDGEMENTS
Social Security, Intergenerational Transfers, and Saving: New Evidence from an Emerging Country

Because of the several shortcomings of aggregate time-series investigations, cross-section studies outnumber the time-series analyses on the relationship between saving and Social Security. This study is the first of its kind for an emerging country that examines the subject at two major points: (1) by using aggregate social security wealth simulations, it formally shows that the PAYG system in Turkey constitutes significant wealth redistributions of resources among different age cohorts; (2) instead of applying traditional wealth functions to observe whether social security wealth displaces non-pension wealth in cross-section setting, it investigates whether or not households’ consumption behavior exhibits a life-cycle pattern by using the Household Labor Force Survey conducted in 2002 for more than eight thousand households. The results confirm that marginal propensity to consume (MPC) out of total resources is significantly different for different age cohorts. Because of its strong Ponzi scheme structure and the fact that it involves resource transfers between different age cohorts we conclude that the Turkish PAYG system may suppress the national saving in Turkey.
Comparative effectiveness of open versus minimally invasive sacroiliac joint fusion

Background The mainstay of sacroiliac joint disruption/degenerative sacroiliitis therapy has been nonoperative management. This nonoperative management often includes a regimen of physical therapy, chiropractic treatment, therapeutic injections, and possibly radiofrequency ablation at the discretion of the treating physician. When these clinical treatments fail, sacroiliac joint fusion has been recommended as the standard treatment. Open and minimally invasive (MIS) surgical techniques are typical procedures. This study aims to compare the perioperative measures and Oswestry Disability Index (ODI) outcomes associated with each of these techniques. Methods A comparative retrospective chart review of patients with sacroiliac joint fusion and a minimum of 1 year of follow-up was performed. Perioperative measures and ODI scores were compared using the Fisher’s exact test and two nonparametric tests, ie, the Mann–Whitney U test and the Wilcoxon signed-rank test. The results are presented as percent or median with range, as appropriate. Results Forty-nine patients from two institutions underwent sacroiliac joint fusion between 2006 and 2012. Ten patients were excluded because of incomplete data, leaving 39 evaluable patients, of whom 22 underwent open and 17 underwent MIS sacroiliac joint fusion. The MIS group was significantly older (median age 66 [39–82] years) than the open group (median age 51 [34–74] years). Surgical time and hospital stay were significantly shorter in the MIS group than in the open group. Preoperative ODI was significantly greater in the open group (median 64 [44–78]) than in the MIS group (median 53 [14–84]). Postoperative improvement in ODI was statistically significant within and between groups, with MIS resulting in greater improvement. Conclusion The open and MIS sacroiliac joint fusion techniques resulted in statistically and clinically significant improvement for patients with degenerative sacroiliitis refractory to nonoperative management. However, the number of patients reaching the minimal clinically important difference and those showing overall improvement were greater in the MIS group.
Bone marrow-derived cells are implicated as a source of lymphatic endothelial progenitors in human breast cancer

Bone marrow-derived endothelial progenitor cells (EPCs) infiltrate into sites of neovascularization in adult tissues and mature into functional blood endothelial cells (BECs) during a process called vasculogenesis. Human marrow-derived EPCs have recently been reported to display a mixed myeloid and lymphatic endothelial cell (LEC) phenotype during inflammation-induced angiogenesis; however, their role in cancer remains poorly understood. We report the in vitro differentiation of human cord blood CD133+CD34+ progenitors into podoplanin+ cells expressing both myeloid markers (CD11b, CD14) and the canonical LEC markers vascular endothelium growth factor receptor 3 (VEGFR-3), lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1), and prospero homeobox 1 (PROX-1). These podoplanin+ cells displayed sprouting behavior comparable to that of LECs in vitro and a dual hemangiogenic and lymphangiogenic activity in vivo in an endothelial cell sprouting assay and corneal vascularization assay, respectively. Furthermore, these cells expressed vascular endothelium growth factor (VEGF) family members A, -C, and -D. Thus, bone-marrow derived EPCs stimulate hemangiogenesis and lymphangiogenesis through their ability to differentiate into LECs and to produce angiogenic factors. Importantly, plasma from patients with breast cancer induced differentiation of CD34+ cord blood progenitors into hemangiogenic and lymphangiogenic CD11b+ myeloid cells, whereas plasma from healthy women did not have this effect. Consistent with these findings, circulating CD11b+ cells from breast cancer patients, but not from healthy women, displayed a similar dual angiogenic activity. Taken together, our results show that marrow-derived EPCs become hemangiogenic and lymphangiogenic upon exposure to cancer plasma. These newly identified functions of bone-marrow derived EPCs are expected to influence the diagnosis and treatment of breast cancer.
Reconstruction of whisper in Chinese by modified MELP

In the present paper, a method for the real-time conversion of whisper to normal phonated speech in Chinese through a multiple excited linear prediction (MELP) analysis-by-synthesis codec is discussed. In the analysis codec processing of whisper speech, parameters from unchanged MELP model are changed, such as the pitch and the formants which aims to reconstruct the target phonated speech using the synthesis codec. Subjective evaluation results show the effectiveness of the technique.
Tethering Complexes in the Arabidopsis Endomembrane System

Targeting of endomembrane transport containers is of the utmost importance for proper land plant growth and development. Given the immobility of plant cells, localized membrane vesicle secretion and recycling are amongst the main processes guiding proper cell, tissue and whole plant morphogenesis. Cell wall biogenesis and modification are dependent on vectorial membrane traffic, not only during normal development, but also in stress responses and in plant defense against pathogens and/or symbiosis. It is surprising how little we know about these processes in plants, from small GTPase regulation to the tethering complexes that act as their effectors. Tethering factors are single proteins or protein complexes mediating first contact between the target membrane and arriving membrane vesicles. In this review we focus on the tethering complexes of the best-studied plant model—Arabidopsis thaliana. Genome-based predictions indicate the presence of all major tethering complexes in plants that are known from a hypothetical last eukaryotic common ancestor (LECA). The evolutionary multiplication of paralogs of plant tethering complex subunits has produced the massively expanded EXO70 family, indicating a subfunctionalization of the terminal exocytosis machinery in land plants. Interpretation of loss of function (LOF) mutant phenotypes has to consider that related, yet clearly functionally-specific complexes often share some common core subunits. It is therefore impossible to conclude with clarity which version of the complex is responsible for the phenotypic deviations observed. Experimental interest in the analysis of plant tethering complexes is growing and we hope to contribute with this review by attracting even more attention to this fascinating field of plant cell biology.
The High Frequency of De novo Promoter Methylation in Synchronous Primary Endometrial and Ovarian Carcinomas

Purpose: The methylation status of hMLH1, CDKN2A, and MGMT was investigated in a panel of synchronous cancers of the ovary and endometrium, fulfilling the clinicopathologic criteria for independent primary tumors to define the possible role of epigenetic mechanisms in the development of these cancers. Experimental Design: Bisulfite-converted DNA from 31 tumors (13 endometrial and 18 ovarian carcinomas) and from matched normal tissue of 13 patients was analyzed by a methylation-specific PCR assay at the CpG-rich 5′ regions of all three genes. In all tumors, we also investigated the presence of microsatellite instability and hMLH1 immunohistochemical expression in relation to hMLH1 hypermethylation status. Results: Methylation of hMLH1, CDKN2A, and MGMT was detected in 39%, 41%, and 48% of endometrial and ovarian tumors, respectively. hMLH1 hypermethylation was observed in all tumors of five patients, and it was invariably associated with loss of hMLH1 protein and presence of microsatellite instability. CDKN2A and MGMT methylation was randomly detected among both endometrial (45% and 24% of cases, respectively) and ovarian carcinomas (39% and 39% of cases, respectively). Concordant methylation at two or three genes was observed in 35% of cases. Conclusions: Epigenetic inactivation of hMLH1, CDKN2A, and MGMT may be a common and early event in the development of synchronous primary endometrial and ovarian carcinomas and may qualify as a marker of a field cancerization encompassing the ovary and endometrium. Detection of MGMT hypermethylation may be useful to define a set of gynecologic malignancies with a specific sensitivity to alkylating chemotherapy.
Back to basics: Analysing the use of research in government public relations campaigns

Public relations plays a critical role in the public and private sectors. To be accountable to government and business, effective public relations campaigns must begin with strong research to guide campaign development. In government and business settings, public relations practitioners use research to define the organisational problem, set appropriate and measurable objectives for campaigns, and identify appropriate strategies. Despite its recognised importance in the academic literature, a major study of Australian public relations campaigns and public relations practitioners’ attitudes towards research in the early 1990s established that research was still talked about much more than it was practised. This study uses the Public Relations Institute of Australia Golden Target Awards collection to examine how Australian government public relations practice uses research in campaign development compared to other categories of practice. The study develops baseline measures of the nature and scope of research methods used in 120 awards submissions from 1997 to 2001. This paper provides an empirical foundation to consider the contribution of different types of research to campaign planning, and examines the consequences of such contribution for government public relations in demonstrating its value.
Further cryptanalysis of ‘A remote authentication scheme using mobile device’

In 2008, Khan et al. proposed a remote user authentication scheme on mobile device, using hash-function and fingerprint biometric. In 2010, Chen et al. discussed some security weaknesses of Khan et al.'s scheme and subsequently proposed an improved scheme. Recently, Truong et al. have demonstrated that in Chen et al.'s scheme, an adversary can successfully replay an intercepted login request. They also showed how an adversary can cheat both the legal participants, by taking advantage of the fact that the scheme does not provide anonymity to the user. In this paper, we show that Chen et al.'s scheme suffers from some additional drawbacks which were not presented by Truong et al. in its analysis.
Digital watermarking based on curvelet transform

This paper proposes a new watermarking method in the curvelet domain. The curvelet transform was developed in order to represent edges along curves much more efficiently than the traditional transforms. We apply the transform to watermarking and evaluate the effectiveness of the method. Our watermarking algorithm embeds a watermark in curvelet coefficients which are selected by a criterion whether they contain as much edge information as possible. We evaluated the effectiveness of the method against some watermark attacks. Experimental results show that the performance of the proposed method against most prominent attacks is good.
Effect of Phellinus baumii-Biotransformed Soybean Powder on Lipid Metabolism in Rats

In this study, we evaluated the hypolipidemic and antioxidative effects of biotransformed soybean powder (BTS; Phellinus baumii-fermented soybean) on lipid metabolism in rats. Sprague-Dawley (SD) male rats were divided into basal diet group (BA), high fat diet group (HF), high fat diet containing 10% BTS group (10 BTS), and high fat diet containing 20% BTS group (20 BTS). Changes in the content of various isoflavones, including daidzein and genistein, within the soybean after fermentation to BTS were investigated. The levels of daidzein and genistein were 149.28 μg/g and 364.31 μg/g, respectively. After six weeks experimental period, Food efficiency ratio in the 10 and 20 BTS group was significantly lower than the HF group (P<0.05). Total serum levels of cholesterol, triglycerides, low-density lipoprotein cholesterol, and atherogenic index ratio in the 10 or 20 BTS group were significantly lower than the HF group. The levels of alanine aminotransferase, aspartate aminotransferase and thiobarbituric acid reactive substance were significantly lower in the groups that received 10% and 20% BTS than the HF. The activities of SOD and CAT were significantly higher in the 10 and 20 BTS group than the HF group. The activity of XO in the 10 and 20 BTS group was significantly lower than in the HF group by 20% and 23%, respectively. In conclusion, these data suggest that BTS is an effective agent in improving lipid metabolism and antioxidant enzyme system.
Mutual exacerbation of peroxisome proliferator‐activated receptor γ coactivator 1α deregulation and α‐synuclein oligomerization

Aggregation of α‐synuclein (α‐syn) and α‐syn cytotoxicity are hallmarks of sporadic and familial Parkinson disease (PD), with accumulating evidence that prefibrillar oligomers and protofibrils are the pathogenic species in PD and related synucleinopathies. Peroxisome proliferator‐activated receptor γ coactivator 1α (PGC‐1α), a key regulator of mitochondrial biogenesis and cellular energy metabolism, has recently been associated with the pathophysiology of PD. Despite extensive effort on studying the function of PGC‐1α in mitochondria, no studies have addressed whether PGC‐1α directly influences oligomerization of α‐syn or whether α‐syn oligomers impact PGC‐1α expression.
A new algorithm for finding enriched regions in ChIP-Seq data

Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. Due to the large amounts of data produced by next generation sequencing, ChIP-Seq offers many advantages, such as much higher resolution, less noise and greater coverage than its predecessor, the ChIP-chip array. Multi-level thresholding algorithms have been applied to many problems in image and signal processing. These algorithms have been used for transcriptomics and genomics data analysis such as sub-grid and spot detection in DNA microarrays, and also for detecting significant regions based on next generation sequencing data. We show that our Optimal Multilevel Thresholding algorithm (OMT) has higher accuracy in detecting enriched regions (peaks) in comparison with previously proposed peak finders by testing three algorithms on the well-known FoxA1 Data set and also for four transcription factors (with a total of six antibodies) for Drosophila melanogaster. Using a small number of parameters is another advantage of the proposed method.
NCK Associated Protein 1 Modulated by miRNA‐214 Determines Vascular Smooth Muscle Cell Migration, Proliferation, and Neointima Hyperplasia

Background MicroRNA miR‐214 has been implicated in many biological cellular functions, but the impact of miR‐214 and its target genes on vascular smooth muscle cell (VSMC) proliferation, migration, and neointima smooth muscle cell hyperplasia is unknown. Methods and Results Expression of miR‐214 was closely regulated by different pathogenic stimuli in VSMCs through a transcriptional mechanism and decreased in response to vascular injury. Overexpression of miR‐214 in serum‐starved VSMCs significantly decreased VSMC proliferation and migration, whereas knockdown of miR‐214 dramatically increased VSMC proliferation and migration. Gene and protein biochemical assays, including proteomic analyses, showed that NCK associated protein 1 (NCKAP1)—a major component of the WAVE complex that regulates lamellipodia formation and cell motility—was negatively regulated by miR‐214 in VSMCs. Luciferase assays showed that miR‐214 substantially repressed wild‐type but not the miR‐214 binding site mutated version of NCKAP1 3′ untranslated region luciferase activity in VSMCs. This result confirmed that NCKAP1 is the functional target of miR‐214 in VSMCs. NCKAP1 knockdown in VSMCs recapitulates the inhibitory effects of miR‐214 overexpression on actin polymerization, cell migration, and proliferation. Data from cotransfection experiments also revealed that inhibition of NCKAP1 is required for miR‐214–mediated lamellipodia formation, cell motility, and growth. Importantly, locally enforced expression of miR‐214 in the injured vessels significantly reduced NCKAP1 expression levels, inhibited VSMC proliferation, and prevented neointima smooth muscle cell hyperplasia after injury. Conclusions We uncovered an important role of miR‐214 and its target gene NCKAP1 in modulating VSMC functions and neointima hyperplasia. Our findings suggest that miR‐214 represents a potential therapeutic target for vascular diseases.
The Nature of Near-Synonymic Relations

1 Introduction The words gawp, gaze, ~md stare all <lenote a, ldnd of prolonge(I look: they a.re nc¢u'-syno'nyms, or plcsionyms [Cruse 1986]. [h)wever, a.s we learn from their indivi(lu;tl enl.ries in the Oxford advanced learner's dictionary (OALD; fourth edi-rio:n, 198f))~ to ga.ze is to look long a.nd steadily; to st;axe is to (Io this with the eyes wide open; a.nd gawping has the additiom~l requirement tha.t the ~ct I)e impolite or stupid. In recent work [l)i-Marco, llirst, m~d Stede 1()93; I)iM~u'co and IIirst 1993], we ddress 1;1l(; problen~ of representing the lexica.l ['ea, tures theft distinguish groups of ne++r-synonynts. Our lexical tim.tures for (lil/erei~Lia.tion are not intended to be any kind of l)rimit;ives for (le(:om-l)ositiomfl semantics: they iir~'(~ ]lOt being used to rel>resent whole meanings, t)ut r+~ther l;o rep]'esent d{[. 'fi'~vnec. ~ between ]ne,~nings. These dift'erences between plesionyms (a ,, I)e sh,~des of (tenota, Lion or (:onnota,tion, or emt)ha.ses on dift'e]'ent (:Oral)O-nen t s o [" t he meani n g. Our eveutuM goM is ~ represent;a.tio], for a lexicon in which sem~mti(" and stylistic distiuctions ca,Jl I)e l/lade bel;ween syn(tttylns a,n(l plesionyms, I)oth within a.nd ~(;ross la.ngua.ges, ['or the purpose of lexica.1 choit:e in natural l,~ngua,ge gener,~tion a, nd machine tra.nslation. The na,ture o[ these distinctions suggests tha.t timy can be viewed a.s rc-lations I)etween nea,r-synot~yms. In this l)a.per, we undertake ~ study of the ch~u'~cteristics of ne~> synonymic rel;~tions as a. stel) towa:r<ls a. knowl edge rel)resent,~tiou for lexi(:M discrimination. As a first st;eli , whi(;h we des(:ribed in [l)iMar(:o, llirst, ~u,d Ste<le 1993], we carried out a. stu<ly o1' dictiona,ry usage notes in order to compile a. list. of the kinds of dime, nsions flint axe used frequently ~s (lenotat;iw; or connot~tive dil[erentiae. We i)r(,-duced zt l>relimina, ry list; of 26 (lenota.tional dimensions and 12 eonnota,tive dimensions (including a few l;h~t we aAded from the discussion on lexi(:a,l a.sl)e(:ts t)y Viua.y m~d l)a.rl)eltmt [1958]). (This set is not, yet; complete 1)1' definitive, of course, bul; we h;we mamtge(t to in(:lu(le ~ fairly (:ompre Imnsive selection of the most common diffexences between ne~r-synonyms.) Some of the dimensions ~re sin@e l)in~u'y choices; others are continuous. We show ;~ representative sa, ml)le in Table 1. l)3a(:h line of the ta£le shows ~ dimension of differentia-lion followed by ex~unple sentences in which two i)lesionyms vary a.long th,~t dimension. 3 Chafl]u and Herrmalan 3.1. Basic theory (]ha,[fin ++nd llerrma.n n [1988] lt~+ve provMed ++ …
Implementing Fast Fourier Transforms on Distributed-Memory Multiprocessors Using Data Redistributions

Implementations of various fast Fourier transform (FFT) algorithms are presented for distributed-memory multiprocessors. These algorithms use data redistribution to localize the computation. The goal is to optimize communication cost by using a minimum number of redistribution steps. Both analytical and experimental performance results on the Intel iPSC/860 system are presented.