Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Density Microwell Chip for Culture and Analysis of Stem Cells

With recent findings on the role of reprogramming factors on stem cells, in vitro screening assays for studying (de)-differentiation is of great interest. We developed a miniaturized stem cell screening chip that is easily accessible and provides means of rapidly studying thousands of individual stem/progenitor cell samples, using low reagent volumes. For example, screening of 700,000 substances would take less than two days, using this platform combined with a conventional bio-imaging system. The microwell chip has standard slide format and consists of 672 wells in total. Each well holds 500 nl, a volume small enough to drastically decrease reagent costs but large enough to allow utilization of standard laboratory equipment. Results presented here include weeklong culturing and differentiation assays of mouse embryonic stem cells, mouse adult neural stem cells, and human embryonic stem cells. The possibility to either maintain the cells as stem/progenitor cells or to study cell differentiation of stem/progenitor cells over time is demonstrated. Clonality is critical for stem cell research, and was accomplished in the microwell chips by isolation and clonal analysis of single mouse embryonic stem cells using flow cytometric cell-sorting. Protocols for practical handling of the microwell chips are presented, describing a rapid and user-friendly method for the simultaneous study of thousands of stem cell cultures in small microwells. This microwell chip has high potential for a wide range of applications, for example directed differentiation assays and screening of reprogramming factors, opening up considerable opportunities in the stem cell field.
Are 'Deep' Parameters Stable? The Lucas Critique as an Empirical Hypothesis

For years, the problems associated with the Lucas critique have loomed over empirical macroeconomics. However, relatively little effort has been devoted to testing the empirical importance of this critique. This paper develops a set of tests for small macroeconometric models, especially those used for monetary policy analysis, and implements them on a set of models used extensively in the literature. In particular, I attempt to test the robustness of optimizing versus non-optimizing models to changes in the monetary policy regime.
Privacy in inter-vehicular networks: Why simple pseudonym change is not enough

Inter-vehicle communication (IVC) systems disclose rich location information about vehicles. State-of-the-art security architectures are aware of the problem and provide privacy enhancing mechanisms, notably pseudonymous authentication. However, the granularity and the amount of location information IVC protocols divulge, enable an adversary that eavesdrops all traffic throughout an area, to reconstruct long traces of the whereabouts of the majority of vehicles within the same area. Our analysis in this paper confirms the existence of this kind of threat. As a result, it is questionable if strong location privacy is achievable in IVC systems against a powerful adversary.
Subepithelial connective tissue grafts in the treatment of multiple recession-type defects.

BACKGROUND There is little documentation regarding the treatment of multiple recession-type defects. The objective of this study was to evaluate the results obtained with a connective tissue graft placed under a coronally advanced flap for the treatment of multiple gingival recessions. METHODS Twenty-eight patients, with at least two recession defects affecting adjacent teeth, were treated with a combination of a connective tissue graft and a coronally advanced flap. At baseline, the following measurements were recorded: 1) recession depth; 2) probing depth; 3) clinical attachment level; and 4) width of keratinized tissue. At 6 months post-surgery, all clinical measurements were repeated. RESULTS The mean root coverage from baseline to 6 months post-surgery results was 96%. Complete root coverage was achieved in 20 (71%) of the 28 defects. The mean recession depth decreased from 3.84 +/- 1.50 mm to 0.14 +/- 0.23 mm. Statistically significant improvements were found for all clinical parameters from baseline to 6 months (P <0.01). Patients with maxillary recessions recorded statistically superior outcomes than patients with mandibular recessions. CONCLUSIONS The results of the present study demonstrated that the connective tissue graft associated with a coronally advance flap is an effective procedure to cover multiple gingival recessions, especially in defects localized in the maxillary arch. However, further investigation focusing on the effects of this root coverage procedure in mandibular sites is necessary.
BIS monitoring during midazolam and midazolam-ketamine conscious intravenous sedation for oral surgery.

OBJECTIVE The purpose of this study was to determine whether the bispectral index scale (BIS) would provide added benefit to established methods of monitoring conscious sedation with midazolam (M group) or midazolam supplemented with ketamine (MK group). STUDY DESIGN BIS was prospectively and blindly examined in 22 patients receiving outpatient oral surgery with conscious sedation supplemented with local anesthesia. RESULTS The average midazolam dose in the midazolam group over the treatment period was 0.01 mg/kg/h, and the average midazolam plus ketamine dose was 0.01 and 0.05 mg/kg/h, respectively. Mean BIS values throughout the sedation study period were 90 for the midazolam group and 94 for the midazolam plus ketamine group. The addition of ketamine did not lower BIS. BIS values did not alter significantly over time except for an expected transient drop after the midazolam bolus induction. CONCLUSION BIS levels remained close to baseline levels, suggesting that BIS would not provided any additional benefit to currently established methods of monitoring patient consciousness during conscious sedation for oral surgery.
Yersinia pestis Lineages in Mongolia

Background Whole genome sequencing allowed the development of a number of high resolution sequence based typing tools for Yersinia (Y.) pestis. The application of these methods on isolates from most known foci worldwide and in particular from China and the Former Soviet Union has dramatically improved our understanding of the population structure of this species. In the current view, Y. pestis including the non or moderate human pathogen Y. pestis subspecies microtus emerged from Yersinia pseudotuberculosis about 2,600 to 28,600 years ago in central Asia. The majority of central Asia natural foci have been investigated. However these investigations included only few strains from Mongolia. Methodology/Principal Findings Clustered Regularly Interspaced Short Prokaryotic Repeats (CRISPR) analysis and Multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) with 25 loci was performed on 100 Y. pestis strains, isolated from 37 sampling areas in Mongolia. The resulting data were compared with previously published data from more than 500 plague strains, 130 of which had also been previously genotyped by single nucleotide polymorphism (SNP) analysis. The comparison revealed six main clusters including the three microtus biovars Ulegeica, Altaica, and Xilingolensis. The largest cluster comprises 78 isolates, with unique and new genotypes seen so far in Mongolia only. Typing of selected isolates by key SNPs was used to robustly assign the corresponding clusters to previously defined SNP branches. Conclusions/Significance We show that Mongolia hosts the most recent microtus clade (Ulegeica). Interestingly no representatives of the ancestral Y. pestis subspecies pestis nodes previously identified in North-western China were identified in this study. This observation suggests that the subsequent evolution steps within Y. pestis pestis did not occur in Mongolia. Rather, Mongolia was most likely re-colonized by more recent clades coming back from China contemporary of the black death pandemic, or more recently in the past 600 years.
A New Original Conception in Rock Magnetism, Paleomagnetism and Geomagnetism: An Origin of the Reversed Magnetization of Rocks on Earth

Abstract So far the field-reversal theory has been accepted to account for the reversed remanent magnetization (RM) of rocks on the Earth. Orlickỳ (2014) revealed a frequent occurrence of the antiferromagnetic (AFM) Fe-Ti oxides in the rocks. Now I have renamed these minerals as the Fe-Ti ferrimagnetic-antiferromagnetic chemical phases (Fe- Ti FriM-AFM ChPs). They may have either cubic spinel, or tetragonal spinel symmetry, respectively. They behave as the Fe-Ti polycrystalline materials. These Fe-Ti FriMAFM ChPs are the two sublattice A and B ChPs, with some specific magnetic behaviour. The titanomagnetite (Ti-Mt, Curie temperature, TC = 230 oC; FriM alignment) and the titanomaghemite (Ti-Mgh, Néel temperature, TN = 450 oC; AFM alignment) containing rocks have been identified as the representants of the the Fe-Ti FriM-AFM cubic spinel ChPs. The interactions with the magnetizing field, with the Weis molecular fields (Weiss-Heisenberg forces) have generated the reversally oriented internal field. The reversally oriented spontaneous magnetization has arosen in the rock. This internal field has been identified as the most important phenomenon leading to the production of the reversally oriented magnetization in the Fe-Ti FriM-AFM ChPs containing rocks. The equations expressing the magnetic behaviour of the magnetic susceptibility (κ) of rocks versus temperature have been derived. The Fe-Ti FriM-AFM cubic spinel can undergone the transition in favour of the Fe-Ti FriM-AFM tetragonal spinel in the rocks, due to a change of the thermodynamic conditions in nature. The reversed RM has supposed been inparted from the Fe-Ti FriM-AFM cubic spinel during this alteration-transition processess. Such tetragonal spinel is more stable and it is able to survive in the rocks in nature. The results of laboratory magnetization of the selected groupings of rocks have been presented below. The basic laboratory methods for the detection of the magnetic behaviour of the Fe-Ti FriM-AFM ChPs containing rocks are described as well. The presented results have shown that we do not need to apply the field reversal theory, because I have revealed the realistic mechanism which is able to generate the reversed RM of rocks under a presence of the normal geomagnetic field.
A robust incomplete factorization preconditioner for positive definite matrices

We describe a novel technique for computing a sparse incomplete factorization of a general symmetric positive definite matrix A. The factorization is not based on the Cholesky algorithm (or Gaussian elimination), but on A‐orthogonalization. Thus, the incomplete factorization always exists and can be computed without any diagonal modification. When used in conjunction with the conjugate gradient algorithm, the new preconditioner results in a reliable solver for highly ill‐conditioned linear systems. Comparisons with other incomplete factorization techniques using challenging linear systems from structural analysis and solid mechanics problems are presented. Copyright © 2003 John Wiley & Sons, Ltd.
A 1-V Process-Insensitive Current-Scalable Two-Stage Opamp With Enhanced DC Gain and Settling Behavior in 65-nm Digital CMOS

A pseudo-cascode compensation technique is proposed to enable a process-insensitive and current-scalable design of the classical two-stage opamp at low supply voltages, without requiring any additional power dissipation. Furthermore, a bulk-biasing technique is proposed to enhance the dc gain of the two-stage opamp, without affecting its output-voltage swing and without requiring any additional power dissipation. To compare the performance advantages of the proposed pseudo-cascode compensation technique versus classical Miller compensation in a two-stage opamp with/without applying the proposed bulk-biasing technique, four opamps were fabricated on the same die in a 1-V 65-nm CMOS process. The corresponding transistors in all four opamps had equal sizes. Furthermore, all four opamps had equal total compensation capacitance and the same total power dissipation. Accordingly, compared to using Miller compensation, by applying the proposed pseudo-cascode-compensation and bulk-biasing techniques in a two-stage opamp, the opamp's dc gain is increased by a factor of 4 (12 dB), its unit-gain frequency is increased by 40%, and its phase margin is maintained over a factor of 100 scaling in its bias current. Furthermore, the overshoot in its large-signal step response is eliminated and the rise/fall settling times are improved by 33%. The trade-off is a minimal decrease in the opamp's phase margin. Importantly, this is all achieved without affecting the opamp's output-voltage swing and without requiring any additional power dissipation.
On the Extent and Origins of Genic Novelty in the Phylum Nematoda

Background The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism. Methods and Findings Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones. Conclusions These classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures.
A Network Biology Approach to Denitrification in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of dissimilatory nitrate reduction to nitrogen gas via nitrite (NO 2), nitric oxide (NO) and nitrous oxide (N 2 O). This study focuses on understanding the influence of environmental conditions on bacterial denitrification performance, using a mathematical model of a metabolic network in P. aeruginosa. To our knowledge, this is the first mathematical model of denitrification for this bacterium. Analysis of the long-term behavior of the network under changing concentration levels of oxygen (O 2), nitrate (NO 3), and phosphate (PO 4) suggests that PO 4 concentration strongly affects denitrification performance. The model provides three predictions on denitrification activity of P. aeruginosa under various environmental conditions, and these predictions are either experimentally validated or supported by pertinent biological literature. One motivation for this study is to capture the effect of PO 4 on a denitrification metabolic network of P. aeruginosa in order to shed light on mechanisms for greenhouse gas N 2 O accumulation during seasonal oxygen depletion in aquatic environments such as Lake Erie (Laurentian Great Lakes, USA). Simulating the microbial production of greenhouse gases in anaerobic aquatic systems such as Lake Erie allows a deeper understanding of the contributing environmental effects that will inform studies on, and remediation strategies for, other hypoxic sites worldwide.
Diagnosis and management of upper extremity deep-vein thrombosis in adults

Summary Upper extremity deep-vein thrombosis (UEDVT) is common and can cause important complications, including pulmonary embolism and post-thrombotic syndrome. An increase in the use of central venous catheters, particularly peripherally inserted central catheters has been associated with an increasing rate of disease. Accurate diagnosis is essential to guide management, but there are limitations to the available evidence for available diagnostic tests. Anticoagulation is the mainstay of therapy, but interventional treatments may be considered in select situations. The risk of UEDVT may be reduced by more careful selection of patients who receive central venous catheters and by use of smaller catheters. Herein we review the diagnosis, management and prevention of UEDVT. Due to paucity of research, some principles are drawn from studies of lower extremity DVT. We present a practical approach to diagnosing the patient with suspected deep-vein thrombosis of the upper extremity.
Transplanting as a means to enhance crop security of fodder beet

Fodder beet has become a popular winter feed for all stock classes in New Zealand. However, poor crop establishment frequently leads to either significant loss in yield, through below-target plant populations, weed competition, or crop failure. This study demonstrates that establishing the crop from transplants, common in the vegetable industry, is one way to achieve a uniform plant population and reduce weed competition through early establishment of canopy cover. The most significant effect of transplant establishment is that the target plant population is readily achieved.
Leptin modulates the expression of catabolic genes in rat nucleus pulposus cells through the mitogen-activated protein kinase and Janus kinase 2/signal transducer and activator of transcription 3 pathways

Obesity has been demonstrated to be involved in the progress of intervertebral disc degeneration (IDD). However, the associated mechanisms remain to be elucidated. The purpose the present study was to examine the effect of leptin on the expression of degeneration-associated genes in rat nucleus pulposus (NP) cells, and determine the possible mechanism. Normal NP cells, obtained from Sprague Dawley rats, were identified using immunocytochemistry for the expression of collagen II and CA125, and treated with leptin and/or interleukin (IL)-β. Subsequently, the mRNA expression levels of matrix metalloproteinase (MMP)-1, MMP-3, MMP-9, MMP-13, a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS)-4, ADAMTS-5, aggrecan and COL2A1 were detected by reverse transcription-quantitative polymerase chain reaction (RT-q-PCR). Alcian staining and immunocytochemistry were used to examine the expression levels of proteoglycan and collagen II. The pathway activation was investigated using western blotting, and inhibitors of the pathways were used to reveal the effect of these pathways on the NP cells. The results of the RT-qPCR demonstrated that leptin alone upregulated the mRNA expression levels of MMP-1, MMP-13, ADAMTS-4, ADAMTS-5 and COL2A1. Synergy of leptin and IL-β was found in the increased expression levels of MMP-1, MMP-3 and ADAMTS-5. The leptin-treated NP cells exhibited decreased expression of collagen II. The mitrogen-activated protein kinase (MAPK) pathway (c-Jun-N-terminal kinase, phosphorylated extracellular signal-regulated kinase and p38), phosphatidylinositol 3-kinase (PI3K)/Akt pathway and Janus kinase (JAK)2/signal transducer and activator of transcription 3 pathway were all activated by leptin, however, inhibitors of all the pathways, with the exception of the PI3K/Akt pathway, reversed the expression levels of MMP-1 and MMP-13. These results suggested that leptin promoted catabolic metabolism in the rat NP cells via the MAPK and JAK2/STAT3 pathways, which may be the mechanism mediating the association between obesity and IDD.
Attributions and Attitudes of Mothers and Fathers in the Philippines

SYNOPSIS Objective. This article investigates the mean level and within-family similarities and differences in Filipino mothers' and fathers' attributions about success and failure in caregiving situations, and their progressive and authoritarian parenting attitudes. Design. Mothers and fathers in 95 families in metropolitan Manila in the Philippines completed interviews. Results. Controlling for parents' age, education, and possible social desirability bias, there was a significant gender difference in modernity of attitudes, with mothers exhibiting higher levels of modernity than fathers. There was a strong correlation in mothers' and fathers' authoritarian attitudes and moderate correlations in modernity of attitudes. There were neither parent gender effects nor concordance in the attributions of mothers and fathers. Conclusions. Cultural explanations are presented to account for the findings, specifically the sociocultural values that foster traditional attitudes favoring parental authority and child obedience, and the differences in gender and family roles of Filipino mothers and fathers.
Uncertainty Estimation by Convolution Using Spatial Statistics

Kriging has proven to be a useful tool in image processing since it behaves, under regular sampling, as a convolution. Convolution kernels obtained with kriging allow noise filtering and include the effects of the random fluctuations of the experimental data and the resolution of the measuring devices. The uncertainty at each location of the image can also be determined using kriging. However, this procedure is slow since, currently, only matrix methods are available. In this work, we compare the way kriging performs the uncertainty estimation with the standard statistical technique for magnitudes without spatial dependence. As a result, we propose a much faster technique, based on the variogram, to determine the uncertainty using a convolutional procedure. We check the validity of this approach by applying it to one-dimensional images obtained in diffractometry and two-dimensional images obtained by shadow moire
Collection devices for human papillomavirus.

BACKGROUND Human papillomavirus (HPV) testing has relied to date on samples collected by experienced health professionals. Self-administered testing devices could allow HPV testing to occur in large-scale epidemiologic studies of primary care screening populations. The purpose of this study is to determine whether a self-collection device for cervicovaginal HPV infection could be developed. METHODS A prospective randomized trial of a consecutive sampling of 93 women, 18 years or older, receiving routine cervical cancer screening and colposcopy in the urban gynecologic clinics in Philadelphia, Pennsylvania, were randomized into 2 arms. Women in arm 1 used a self-administered tampon before the physician-directed swabs of the cervix; in arm 2, women underwent the physician-directed swab testing before using the self-administered tampon. The concordance of HPV DNA positivity between sampling methods detected by a Hybrid Capture HPV tube test for both low- and high-risk types of HPV was the main outcome measure. RESULTS The concordance rate (ie, women whose cultures were classified as negative on both tests or positive on both tests) for arms 1 and 2 were similar: 78.3% and 80.9%, respectively. CONCLUSIONS The tampon was equivalent to the physician-directed swab in HPV detection and suggests its feasibility in long-term primary care studies of screening populations.