Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells

BACKGROUND Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation. Although MDA-based WGA yielded the highest DNA amount, DNA quality was not adequate for downstream analysis. PCR-based WGA demonstrates superiority over MDA-PCR combining technique for SNP and indel analysis in single cells. However, SNP calling performance of MDA-PCR WGA improves with increasing amount of input DNA, whereas CNA analysis does not. The performance of PCR-based WGA did not significantly improve with increase of input material. CNA profiles of single cells, amplified with MDA-PCR technique and sequenced on both HiSeq2000 and IonProton platforms, resembled unamplified DNA the most. MATERIALS AND METHODS We analyzed the performance of PCR-based, multiple-displacement amplification (MDA)-based, and MDA-PCR combining WGA techniques (WGA kits Ampli1, REPLI-g, and PicoPlex, respectively) on single and pooled tumor cells obtained from EDTA- and CellSave-preserved blood and archival material. Amplified DNA underwent exome-Seq with the Illumina HiSeq2000 and ThermoFisher IonProton platforms. CONCLUSION We demonstrate the feasibility of single cell genotyping of differently preserved material, nevertheless, WGA and NGS approaches have to be chosen carefully depending on the study aims.
Gene expression signatures in tree shrew sclera in response to three myopiagenic conditions.

PURPOSE We compared gene expression signatures in tree shrew sclera produced by three different visual conditions that all produce ocular elongation and myopia: minus-lens wear, form deprivation, and dark treatment. METHODS Six groups of tree shrews (n = 7 per group) were used. Starting 24 days after normal eye-opening (days of visual experience [DVE]), two minus-lens groups wore a monocular -5 diopter (D) lens for 2 days (ML-2) or 4 days (ML-4); two form-deprivation groups wore a monocular translucent diffuser for 2 days (FD-2) or 4 days (FD-4). A dark-treatment (DK) group was placed in continuous darkness for 11 days after experiencing a light/dark environment until 17 DVE. A normal colony-reared group was examined at 28 DVE. Quantitative PCR was used to measure the relative differences in mRNA levels for 55 candidate genes in the sclera that were selected, either because they showed differential expression changes in previous ML studies or because a whole-transcriptome analysis suggested they would change during myopia development. RESULTS The treated eyes in all groups responded with a significant myopic shift, indicating that the myopia was actively progressing. In the ML-2 group, 27 genes were significantly downregulated in the treated eyes, relative to control eyes. In the treated eyes of the FD-2 group, 16 of the same genes also were significantly downregulated and one was upregulated. The two gene expression patterns were significantly correlated (r(2) = 0.90, P < 0.001). After 4 days of treatment, 31 genes were significantly downregulated in the treated eyes of the ML-4 group and three were upregulated. Twenty-nine of the same genes (26 down- and 3 up-regulated) and six additional genes (all downregulated) were significantly affected in the FD-4 group. The response patterns were highly correlated (r(2) = 0.95, P < 0.001). When the DK group (mean of right and left eyes) was compared to the control eyes of the ML-4 group, the direction and magnitude of the gene expression patterns were similar to those of the ML-4 (r(2) = 0.82, P < 0.001, excluding PENK). Similar patterns also were found when the treated eyes of the ML-4, FD-4, and DK groups were compared to the age-matched normal eyes. CONCLUSIONS The very similar gene expression signatures produced in the sclera by the three different myopiagenic visual conditions at different time points suggests that there is a "scleral remodeling signature" in this mammal, closely related to primates. The scleral genes examined did not distinguish between the specific visual stimuli that initiate the signaling cascade that results in axial elongation and myopia.
Funding optimization for a bank integrating credit and liquidity risk

In this paper we apply two optimization frameworks to determineÂ the optimal wholesale funding mix of a bank given uncertainty in bothÂ credit and liquidity risk. A stochastic linear programming method isÂ used to find the optimal strategy to be maintained across all scenarios. Â A recursive learning method is developed to provide the bank withÂ a trading signal to dynamically adjust the wholesale funding mix asÂ the macroeconomic environment changes. The performance of the twoÂ methodologies is compared in the final section.Mathematics Subject Classification: C61, G21, C53Keywords: Bank Funding, Optimization, Credit Risk, Liquidity Risk
Electron beam computed tomography and coronary artery disease: scanning for coronary artery calcification.

OBJECTIVE To review the association of coronary artery calcification with coronary atherosclerosis and its potential clinical application as detected on electron beam computed tomography (EBCT). DESIGN A literature review of coronary artery calcification, coronary artery disease, and EBCT is presented, and clinical applications of EBCT are discussed. RESULTS Recent studies have confirmed that arterial calcification is an active process intimately associated with atherosclerotic plaque evolution. Clinical investigations with use of EBCT have shown that a scan "negative" for coronary calcification is common in patients with normal or near-normal findings on coronary angiography, whereas patients with severe obstructive disease most commonly have "positive" scans--greater amounts of coronary artery calcium are associated with more severe luminal disease. Coronary artery calcium as evaluated on EBCT follows patterns that reflect the development of coronary atheromatous disease as a function of age and gender. Although histologic studies have confirmed that not all atherosclerotic segments have detectable calcification, the area of coronary artery calcification quantified on EBCT has a direct, positive relationship with the histopathologic coronary plaque area. CONCLUSION The long-held notion of "degenerative" calcification of the coronary arteries with aging is incorrect. Although the incidence of coronary artery calcification increases with patient age, this relationship simply parallels the increased incidence of coronary atherosclerosis with advancing age. Data suggest that EBCT is a highly sensitive and specific test for coronary atherosclerosis and provide a basis for clinical applications when EBCT is viewed as a noninvasive method to estimate human coronary atherosclerotic involvement and "plaque burden. "
Alter(n)ative Literacies: Elementary Teachers' Practices with Culturally and Linguistically Diverse students in one French-language School in Ontario

This case study was conducted in one elementary French-language school in Ontario with 1 administrator, 4 teachers and their culturally and linguistically diverse (CLD) students. Through the integration of bhabha’s (1994) notion of Third space, multiple literacies theory (Cummins, 2001; Masny 2009) and by drawing on interviews, observations, and students’ work samples, I conceptualise an alter(n)ative literacies framework to address growing diversity in French-language schools. The term alter(n)ative is developed to express the intertwined benefit of expanding traditional notions of literacy to include alternative language practices and the potential alter-ative effect of re-envisioning the resources children bring to their literacy and language development at school. This thesis argues that teachers can critically (re)interprete official policies concerning Frenchlanguage schools in order to effectively foster students’ alter(n)ative literacies development. In doing so, teachers affirm the plurality of students’ multiple identities as a foundation for their participation within evolving cosmopolitan franco-ontarian
Leaching of S-metolachlor, terbuthylazine, desethyl-terbuthylazine, mesotrione, flufenacet, isoxaflutole, and diketonitrile in field lysimeters as affected by the time elapsed between spraying and first leaching event

The effect of elapsed time between spraying and first leaching event on the leaching behavior of five herbicides (terbuthylazine, S-metolachlor, mesotrione, flufenacet, and isoxaflutole) and two metabolites (desethyl-terbuthylazine and diketonitrile) was evaluated in a 2011–2012 study in northwest Italy. A battery of 12 lysimeters (8.4 m2 long with a depth of 1.8 m) were used in the study, each filled with silty-loam soil and treated during pre-emergence with the selected herbicides by applying a mixture of commercial products Lumax (4 L ha−1) and Merlin Gold (1 L ha−1). During treatment periods, no gravity water was present in lysimeters. Irrigation events capable of producing leaching (40 mm) were conducted on independent groups of three lysimeters on 1 day after treatment (1 DAT), 7 DAT, 14 DAT, and 28 DAT. The series was then repeated 14 days later. Leachate samples were collected a few days after irrigation; compounds were extracted by solid phase extraction and analyzed by high-performance liquid chromatography and gas chromatography–mass spectrometry. Under study conditions, terbuthylazine and S-metolachlor showed the highest leaching potentials. Specifically, S-metolachlor concentrations were always found above 0.25 µg L−1. Desethyl-terbuthylazine was often detected in leached waters, in most cases at concentrations above 0.1 µg L−1. Flufenacet leached only when irrigation occurred close to the time of herbicide spraying. Isoxaflutole and mesotrione were not measured (<0.1 µg L−1), while diketonitrile was detected in concentrations above 0.1 µg L−1 on 1 DAT in 2011 only.
Sperm competition influences sperm size in mammals

Among mammals sperm competition leads to selection for increased sperm numbers but it is not known whether it also leads to changes in sperm size. Two contrasting theoretical predictions have been made. The first hypothesis relies on the assumption that there is a trade-off between sperm numbers and sperm size and predicts that, in species confronting sperm competition, there will be a concomitant decrease in sperm size as sperm numbers increase. In contrast, the second hypothesis suggests that longer sperm may outcompete rival sperm; if longer sperm may swim faster, they will reach the ova sooner and will be selected when sperm competition prevails. We tested these hypotheses in both primates and rodents. We report that males from species in which females mate promiscuously have longer sperm than species in which females mate with one male. In addition, we also found that sperm length is positively correlated with maximum sperm velocity. Our findings thus support the view that longer sperm may be adaptive in the context of sperm competition.
Thermal conductivity measurements of 2D complex liquids using nonequilibrium molecular dynamics simulations

We have been analyzed heat conductivity of two-dimensional (2D) strongly-coupled complex (dusty) plasma liquids (SCCDPLs), regarding them as systems composed of charged dust particles with hard cores interacting through the repulsive Yukawa potential contribution taking into account, for the first time. In this paper, homogenous nonequilibrium molecular dynamics (HNEMD) simulation has been conducted for 2D SCCDPL systems under near-equilibrium external force field strength (Fex). The new improved HNEMD algorithm is found to have more comparable performance with the earlier equilibrium molecular dynamics (EMD) than that of earlier Inhomogenous nonequilibrium molecular dynamics (InHNEMD) for 2D Yukawa Liquid systems. Different sequence of the thermal conductivity (λ0) corresponding to a decreasing and increasing sequence of applied external field force strength (Fex) has been checked in order to determine near-equilibrium λ0 in linear regime of the SCCDPLs. The New simulation results computed with fixed external field strengths are in practical agreement with earlier experimental and numerical data points within less than ±15% for most of the present data point. It was shown that the HNEMD algorithm was a powerful tool for computing and exploring the behavior of λ0 of SCCDPLs for the complete range of plasma states (Γ, κ) than those calculated in previous works, based on different numerical methods.
Effect of surgery on monocyte function

In vitro monocyte lysozyme production (IVMLP) was assessed in 10 male patients preoperatively and at intervals postoperatively. A similar procedure was carried out in 6 sex‐ and age‐matched controls. In contrast to the control group where the IVMLP was constant, the IVLMP levels in the surgical group showed a marked increase at 6–10 h postoperatively, falling to control levels after 10 days. In addition, peripheral monocyte counts were carried out using a Technicon Hemalog D counter which produces accurate reproducible counts for cells such as monocytes which occur at low frequency. The peripheral monocyte counts were stable in the control group, whilst in the surgical patients there were significantly higher readings at 36–48 h, which persisted for up to 10 days compared with preoperative counts. This study suggests that surgery has both a qualitative (IVMLP) and quantitative (monocyte counts) effect on the mononuclear phagocytes. These data may be relevant when considering factors that influence the early stages of wound healing.
Neural Processes Distinguishing Elite from Expert and Novice Athletes

This commentary builds on a companion article in which Kim et al compare brain activation in elite, expert, and novice archers during a simulated target aiming task (Kim et al. 2014. Cogn Behav Neurol. 27:173-182). With the archery study as our starting point, we address 4 neural processes that may be responsible in general for elite athletes’ superior performance over experts and novices: neural efficiency, cortical expansion, specialized processes, and internal models. In Kim et al’s study, the elite archers’ brains showed more activity in the supplementary motor area and the cerebellum than those of the novices and experts, and showed minimal widespread activity, especially in frontal areas involved with executive control. Kim et al’s results are consistent with the idea of specialized neural processes that help coordinate motor planning and control. As athletes become more skilled, these processes may mediate the reduction in widespread activity in regions mapping executive control, and may produce a shift toward more automated processing. Kim et al’s finding that activity in the cerebellum rose with increasing skill is consistent both with expansion of the finger representational area in the cerebellum and with internal models that simulate how archers manipulate the bow and arrow when aiming. Kim et al prepare the way for testing of neuromodulation techniques to improve athletic performance, refine highly technical job skills, and rehabilitate patients.
Electronic Government at the Local Level

Much like businesses with electronic commerce, public organizations are beginning to embrace electronic government (e-government). This article defines the term e-government, discusses the literature oflocal-Ievel e-government, and documents the adoption and sophistication of e-government among U.S. local governments. It employs data from a survey conducted in 2000 to examine local adoption of e-government. E-government adoption among local governments generally tracks previously documented patterns of information technology adoption, which show a statistically significant relationship between adoption and such demographic variables as population size, form and type of government, region, and metro status. The article compares the results of that survey to a normative model of e-government maturity and finds that the emergence of e-government at the local level is still in its formative stages. The analysis also examines perceived impacts from e-govemment, sophistication of e-government offerings, barrier.
A Direct Interaction between the Aryl Hydrocarbon Receptor and Retinoblastoma Protein

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor in eukaryotic cells that alters gene expression in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In 5L hepatoma cells, TCDD induces a G1 cell cycle arrest through a mechanism that involves the AhR. The retinoblastoma tumor suppressor protein (pRb) controls cell cycle progression through G1 in addition to promoting differentiation. We examined whether the human AhR or its dimerization partner, the AhR nuclear translocator, interacts with pRb as a basis of the TCDD-induced cell cycle arrest.In vivo and in vitro assays reveal a direct interaction between pRb and the AhR but not the AhR nuclear translocator protein. Binding between the AhR and pRb occurs through two distinct regions in the AhR. A high affinity site lies within the N-terminal 364 amino acids of the AhR, whereas a lower affinity binding region colocalizes with the glutamine-rich transactivation domain of the receptor. AhR ligand binding is not required for the pRb interaction per se, although immunoprecipitation experiments in 5L cells reveal that pRb associates preferentially with the liganded AhR, consistent with a requirement for ligand-induced nuclear translocation. These observations provide a mechanistic insight into AhR-mediated cell cycle arrest and a new perspective on TCDD-induced toxicity.
Interference alignment based dynamic TDD for small cells

Dynamic time-division-duplexing (TDD) uplink (UL) and downlink (DL) reconfiguration is a promising solution to the problem of traffic adaptation in future small cell deployment, wherein the traffic demand may vary dynamically in volume and in transmission direction. Applying dynamic TDD UL-DL reconfiguration in a multi-cell scenario may lead to new challenges caused by inter-cell interference. In this paper, we propose an interference alignment based multiple-input-multiple-output (MIMO) transmission scheme that effectively addresses the interference problem in dynamic TDD systems and improves the system capacity. The proposed scheme may be relevant to 3GPP LTE standardization of enhanced interference mitigation and traffic adaptation (eIMTA), small cell enhancement and coordinated multi-point (CoMP) topics.
Mechanistic insights into cellular alteration of prion by poly‐D‐lysine: the role of H2H3 domain

Misfolding of the prion protein (PrP) is the central feature of prion diseases. The conversion of the normal α‐helical PrPC into a pathological β‐en‐riched PrPSc constitutes an early event in the infectious process. Several hypotheses, involving different regions of the protein, endeavor to delineate the structural mechanism underlying this change of conformation. All current working hypotheses, however, are based on biophysical and modeling studies, the biological relevance of which still needs to be assessed. We have studied the effect of positively charged polymers on the conversion, using polylysine as a model system, and have investigated a possible mechanism of structural stabilization. We have shown that poly‐d‐lysine removes proteinase K‐resistant PrP from prion‐infected SN56 neuroblastoma cells without affecting PrPC. The effect is enantiospecific since the levorotary isomer, poly‐l‐lysine, has a markedly weaker effect, likely because of its higher susceptibility to degradation. In vitro cross‐linking and NMR studies confirm a direct interaction between polylysine and PrP, which mainly maps to the PrP region containing helices 2 and 3 (H2H3). Interaction prevents conformational conversion and protein aggregation. Our results establish a central role of H2H3 in PrPSc amyloidogenesis and replication and provide biological relevance for the pathological misfolding of this domain. —Xu, Z. , Adrover, M. , Pastore, A. , Prigent, S. , Mouthon, F. , Comoy, E. , Rezaei, H. , Deslys, J. ‐P. Mechanistic insights into cellular alteration of prion by poly‐D‐lysine: the role of H2H3 domain. FASEB J. 25, 3426–3435 (2011). www.fasebj. org
DNA sequences similar to those of simian virus 40 in ependymomas and choroid plexus tumors of childhood.

BACKGROUND Ependymomas and papillomas of the choroid plexus occur in early childhood. The ubiquitous human polyomaviruses, BK virus and JC virus, have been associated with the induction of these neoplasms in animal models. A related monkey polyomavirus, simian virus 40 (SV40), is highly tumorigenic in rodents and also induces choroid plexus papillomas. METHODS We tested the possibility that polyomaviruses were associated with these tumors in humans. Tumors from 31 children--20 with choroid plexus neoplasms and 11 with ependymomas--were evaluated for the presence of polyomavirus T-antigen gene sequences by means of amplification with the polymerase chain reaction. RESULTS Ten of the 20 choroid plexus tumors and 10 of the 11 ependymomas contained amplification products that preferentially hybridized to probes specific for SV40 viral DNA rather than BK or JC viral DNA. In two specimens, DNA sequencing demonstrated that the amplified sequence was identical to the sequence of that region of the SV40 gene. In three other specimens, amplification with SV40-specific primers revealed a 574-bp segment of the SV40 viral gene. In 7 of 11 tumors examined by immunohistochemical staining, viral T antigen was expressed in the nuclei of the neoplastic cells. CONCLUSIONS Half of the choroid plexus tumors and most of the ependymomas that we studied contained and expressed a segment of T-antigen gene related to SV40. These results suggest that SV40 or a closely related virus may have an etiologic role in the development of these neoplasms during childhood, as in animal models.
The JAK-STAT Signaling Pathway: Input and Output Integration1

Universal and essential to cytokine receptor signaling, the JAK-STAT pathway is one of the best understood signal transduction cascades. Almost 40 cytokine receptors signal through combinations of four JAK and seven STAT family members, suggesting commonality across the JAK-STAT signaling system. Despite intense study, there remain substantial gaps in understanding how the cascades are activated and regulated. Using the examples of the IL-6 and IL-10 receptors, I will discuss how diverse outcomes in gene expression result from regulatory events that effect the JAK1-STAT3 pathway, common to both receptors. I also consider receptor preferences by different STATs and interpretive problems in the use of STAT-deficient cells and mice. Finally, I consider how the suppressor of cytokine signaling (SOCS) proteins regulate the quality and quantity of STAT signals from cytokine receptors. New data suggests that SOCS proteins introduce additional diversity into the JAK-STAT pathway by adjusting the output of activated STATs that alters downstream gene activation.