Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic profiling reveals an alarming rate of cross‐contamination among human cell lines used in China

Cell lines are widely used as in vitro model systems in biologic and medical research. However, much of the research has been invalidated by the unwitting use of false cell lines. A significant proportion of the research involving human cell lines was initiated in China. Paradoxically, the cell lines used in China have never been authenticated. Here, we present a comprehensive survey of cross‐contamination in 380 samples from 113 independent sources in China using short tandem repeat profiling methods. High levels of cross‐contamination were uncovered (95 of 380, 25%). Notable false cell lines (e.g., KB and WISH) are still actively used under their false identity and tissue attributions. Most strikingly, 85.51% of lines established in China were misidentified (59 of 69) and accounted for over half of the misidentifications (59 of 95, 62.11%). Further, 93.22% of the contaminants in cell lines established in laboratories of China were HeLa cells or a possible hybrid of HeLa with an unknown cell line. Results from these misidentified lines have been published in thousands of potentially erroneous articles and may have distorted the findings visible to the scientific community. False lines have been used in drug screening, potentially leading to unusable or even harmful therapeutic strategies. We also noted the causes of contamination and provided suggestions for remediation. —Ye, F. , Chen, C, Qin, J., Liu, J., Zheng, C. Genetic profiling reveals an alarming rate of cross‐contamination among human cell lines used in China. FASEB J. 29, 4268‐4272 (2015). www.fasebj. org
DS-OCDMA receivers based on parallel interference cancellation and hard limiters

In an incoherent direct-sequence optical code-division multiple-access (DS-OCDMA) system, multiple-access interference (MAI) is one of the principal limitations. To mitigate MAI, the parallel interference cancellation (PIC) technique can be used to remove nondesired users' contribution. In this paper, we study four DS-OCDMA receivers based on the PIC technique with hard limiters placed before the nondesired users or before the desired user receiver, or both. We develop, for the ideal synchronous case, the theoretical upper bound of the error probability for the four receivers. Significant performance improvement is obtained by comparison with conventional receivers in the case of optical orthogonal codes. The paper highlights that the number of active users with null error probability is doubled, compared with conventional receivers. Finally, we show that, thanks to their good performances, the PIC structures permit considerably reducing the minimal code length required to have 30 users with bit-error rate <10 -9. So, the hardware constraints are relaxed for realistic application
Adaptive context features for toponym resolution in streaming news

News sources around the world generate constant streams of information, but effective streaming news retrieval requires an intimate understanding of the geographic content of news. This process of understanding, known as geotagging, consists of first finding words in article text that correspond to location names (toponyms), and second, assigning each toponym its correct lat/long values. The latter step, called toponym resolution, can also be considered a classification problem, where each of the possible interpretations for each toponym is classified as correct or incorrect. Hence, techniques from supervised machine learning can be applied to improve accuracy. New classification features to improve toponym resolution, termed adaptive context features, are introduced that consider a window of context around each toponym, and use geographic attributes of toponyms in the window to aid in their correct resolution. Adaptive parameters controlling the window's breadth and depth afford flexibility in managing a tradeoff between feature computation speed and resolution accuracy, allowing the features to potentially apply to a variety of textual domains. Extensive experiments with three large datasets of streaming news demonstrate the new features' effectiveness over two widely-used competing methods.
Operator norm consistent estimation of large-dimensional sparse covariance matrices

Estimating covariance matrices is a problem of fundamental importance in multivariate statistics. In practice it is increasingly frequent to work with data matrices X of dimension n x p, where p and n are both large. Results from random matrix theory show very clearly that in this setting, standard estimators like the sample covariance matrix perform in general very poorly. In this "large n, large p" setting, it is sometimes the case that practitioners are willing to assume that many elements of the population covariance matrix are equal to 0, and hence this matrix is sparse. We develop an estimator to handle this situation. The estimator is shown to be consistent in operator norm, when, for instance, we have p ? n as n → oo. In other words the largest singular value of the difference between the estimator and the population covariance matrix goes to zero. This implies consistency of all the eigenvalues and consistency of eigenspaces associated to isolated eigenvalues. We also propose a notion of sparsity for matrices, that is, "compatible" with spectral analysis and is independent of the ordering of the variables.
A fast prototyping process for fabrication of microfluidic systems on soda-lime glass

This paper describes a fast, low-cost but reliable process for the fabrication of microfluidic systems on soda-lime glass substrates. Instead of using an expensive metal or polisilicon/nitride layer as an etch mask, a thin layer of AZ 4620 positive photoresist (PR) is used for buffered oxide etching (BOE) of soda-lime glass. A novel two-step baking process prolongs the survival time of the PR mask in the etchant, which avoids serious peeling problems of the PR. A new process to remove precipitated particles generated during the etching process is also reported in which the glass substrate is dipped into a 1 M hydrochloride solution. A microfluidic channel with a depth of 35.95±0.39 µm is formed after 40 min BOE in an ultrasonic bath. The resulting channel has a smooth profile with a surface roughness of less than 45.95±7.96 A. Glass chips with microfluidic channels are then bonded at 580 °C for 20 min to seal the channel while a slight pressure is applied. A new bonding process has been developed such that the whole process can be finished within 10 h. To our knowledge, this is the shortest processing time that has ever been reported. In the present study, an innovative microfluidic device, a `micro flow-through sampling chip', has been demonstrated using the fabrication method. Successful sampling and separation of Cy5-labelled bovine serum albumin (BSA) and anti-BSA has been achieved. This simple fabrication process is suitable for fast prototyping and mass production of microfluidic systems.
Neural Dissociations between Action Verb Understanding and Motor Imagery

According to embodied theories of language, people understand a verb like throw, at least in part, by mentally simulating throwing. This implicit simulation is often assumed to be similar or identical to motor imagery. Here we used fMRI to test whether implicit simulations of actions during language understanding involve the same cortical motor regions as explicit motor imagery. Healthy participants were presented with verbs related to hand actions (e.g., to throw) and nonmanual actions (e.g., to kneel). They either read these verbs (lexical decision task) or actively imagined performing the actions named by the verbs (imagery task). Primary motor cortex showed effector-specific activation during imagery, but not during lexical decision. Parts of premotor cortex distinguished manual from nonmanual actions during both lexical decision and imagery, but there was no overlap or correlation between regions activated during the two tasks. These dissociations suggest that implicit simulation and explicit imagery cued by action verbs may involve different types of motor representations and that the construct of “mental simulation” should be distinguished from “mental imagery” in embodied theories of language.
Economic Analysis of Pandemic Influenza Vaccination Strategies in Singapore

Background All influenza pandemic plans advocate pandemic vaccination. However, few studies have evaluated the cost-effectiveness of different vaccination strategies. This paper compares the economic outcomes of vaccination compared with treatment with antiviral agents alone, in Singapore. Methodology We analyzed the economic outcomes of pandemic vaccination (immediate vaccination and vaccine stockpiling) compared with treatment-only in Singapore using a decision-based model to perform cost-benefit and cost-effectiveness analyses. We also explored the annual insurance premium (willingness to pay) depending on the perceived risk of the next pandemic occurring. Principal Findings The treatment-only strategy resulted in 690 deaths, 13,950 hospitalization days, and economic cost of USD$497 million. For immediate vaccination, at vaccine effectiveness of >55%, vaccination was cost-beneficial over treatment-only. Vaccine stockpiling is not cost-effective in most scenarios even with 100% vaccine effectiveness. The annual insurance premium was highest with immediate vaccination, and was lower with increased duration to the next pandemic. The premium was also higher with higher vaccine effectiveness, attack rates, and case-fatality rates. Stockpiling with case-fatality rates of 0.4–0.6% would be cost-beneficial if vaccine effectiveness was >80%; while at case-fatality of >5% stockpiling would be cost-beneficial even if vaccine effectiveness was 20%. High-risk sub-groups warrant higher premiums than low-risk sub-groups. Conclusions The actual pandemic vaccine effectiveness and lead time is unknown. Vaccine strategy should be based on perception of severity. Immediate vaccination is most cost-effective, but requires vaccines to be available when required. Vaccine stockpiling as insurance against worst-case scenarios is also cost-effective. Research and development is therefore critical to develop and stockpile cheap, readily available effective vaccines.
AutoMan: a platform for integrating human-based and digital computation

Humans can perform many tasks with ease that remain difficult or impossible for computers. Crowdsourcing platforms like Amazon's Mechanical Turk make it possible to harness human-based computational power at an unprecedented scale. However, their utility as a general-purpose computational platform remains limited. The lack of complete automation makes it difficult to orchestrate complex or interrelated tasks. Scheduling more human workers to reduce latency costs real money, and jobs must be monitored and rescheduled when workers fail to complete their tasks. Furthermore, it is often difficult to predict the length of time and payment that should be budgeted for a given task. Finally, the results of human-based computations are not necessarily reliable, both because human skills and accuracy vary widely, and because workers have a financial incentive to minimize their effort. This paper introduces AutoMan, the first fully automatic crowdprogramming system. AutoMan integrates human-based computations into a standard programming language as ordinary function calls, which can be intermixed freely with traditional functions. This abstraction lets AutoMan programmers focus on their programming logic. An AutoMan program specifies a confidence level for the overall computation and a budget. The AutoMan runtime system then transparently manages all details necessary for scheduling, pricing, and quality control. AutoMan automatically schedules human tasks for each computation until it achieves the desired confidence level; monitors, reprices, and restarts human tasks as necessary; and maximizes parallelism across human workers while staying under budget.
Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds

We conducted a structural genomics analysis of the folds and structural superfamilies in the first 20 completely sequenced genomes by focusing on the patterns of fold usage and trying to identify structural characteristics of typical and atypical folds. We assigned folds to sequences using PSI‐blast, run with a systematic protocol to reduce the amount of computational overhead. On average, folds could be assigned to about a fourth of the ORFs in the genomes and about a fifth of the amino acids in the proteomes. More than 80% of all the folds in the SCOP structural classification were identified in one of the 20 organisms, with worm and E. coli having the largest number of distinct folds. Folds are particularly effective at comprehensively measuring levels of gene duplication, because they group together even very remote homologues. Using folds, we find the average level of duplication varies depending on the complexity of the organism, ranging from 2.4 in M. genitalium to 32 for the worm, values significantly higher than those observed based purely on sequence similarity. We rank the common folds in the 20 organisms, finding that the top three are the P‐loop NTP hydrolase, the ferrodoxin fold, and the TIM‐barrel, and discuss in detail the many factors that affect and bias these rankings. We also identify atypical folds that are “unique” to one of the organisms in our study and compare the characteristics of these folds with the most common ones. We find that common folds tend be more multifunctional and associated with more regular, “symmetrical” structures than the unique ones. In addition, many of the unique folds are associated with proteins involved in cell defense (e.g., toxins). We analyze specific patterns of fold occurrence in the genomes by associating some of them with instances of horizontal transfer and others with gene loss. In particular, we find three possible examples of transfer between archaea and bacteria and six between eukarya and bacteria. We make available our detailed results at http://genecensus.org/20. Proteins 2002;47:126–141. © 2002 Wiley‐Liss, Inc.
Release of Calcium from Inositol 1,4,5-Trisphosphate Receptor-Regulated Stores by HIV-1 Tat Regulates TNF-α Production in Human Macrophages1

HIV-1 protein Tat is neurotoxic and increases macrophage and microglia production of TNF-α, a cytopathic cytokine linked to the neuropathogenesis of HIV dementia. Others have shown that intracellular calcium regulates TNF-α production in macrophages, and we have shown that Tat releases calcium from inositol 1,4,5-trisphosphate (IP3) receptor-regulated stores in neurons and astrocytes. Accordingly, we tested the hypothesis that Tat-induced TNF-α production was dependent on the release of intracellular calcium from IP3-regulated calcium stores in primary macrophages. We found that Tat transiently and dose-dependently increased levels of intracellular calcium and that this increase was blocked by xestospongin C, pertussis toxin, and by phospholipase C and type 1 protein kinase C inhibitors but not by protein kinase A or phospholipase A2 inhibitors. Xestospongin C, BAPTA-AM, U73122, and bisindolylmalemide significantly inhibited Tat-induced TNF-α production. These results demonstrate that in macrophages, Tat-induced release of calcium from IP3-sensitive intracellular stores and activation of nonconventional PKC isoforms play an important role in Tat-induced TNF-α production.
How strict are theoretical bounds for dielectric properties of mixtures?

This report discusses bounds for mixing rules. Several theoretical bounds and limits for the effective permittivity of heterogeneous media have been derived. However, it may happen that the bounds are trespassed in the real-life applications. Examples of such behavior are given for snow, random media simulations, lossy heterogeneous materials, and magnetic and magnetoelectric materials. Reasons for the bound-violation phenomenon are discussed.
Dielectric properties of BNT-xBT prepared by hydrothermal process

The BNT ceramic sample might be a good replacement for PZT piezoelectric in industrial applications, especially in energy harvesting from crystal vibrations. In order to enhance the performance of BNT ceramic, the solid solution was chosen by substitution with Ba+2 at Morphtropic Phase Boundary (MPB). The BNT-xBT powders with x=1, 0.07, 0.06 and 0 were prepared by the hydrothermal method with average particle size (65–150nm) at (90∘C/72h). The ceramic disc was sintered at (1150∘C/4h) and showed excellent relative density of about 96%. The results of X-ray diffraction (XRD) confirmed the MPB for x=0.06 and 0.07, while the BNT had a rhombohedral structure and BT had a tetragonal structure. The dielectric measurements showed that BNT, BNT-7BT, BNT-6BT behave as the relaxator ferroelectric and showed a strong dependence on frequency, especially in the MPB region while BT behaves as a normal ferroelectric. Both the Curie temperature and depolarization temperature decrease at the MPB region and showed strong dependency on frequency.
High-Throughput Mutation Profiling Identifies Frequent Somatic Mutations in Advanced Gastric Adenocarcinoma

Background Gastric cancer is one of the leading cancer types in incidence and mortality, especially in Asia. In order to improve survival, identification of a catalogue of molecular alterations underlying gastric cancer is a critical step for developing and designing genome-directed therapies. Methodology/Principal Findings The Center for Cancer Genome Discovery (CCGD) at the Dana-Farber Cancer Institute (DFCI) has adapted a high-throughput genotyping platform to determine the mutation status of a large panel of known cancer genes. The mutation detection platform, termed OncoMap v4, interrogates 474 “hotspot” mutations in 41 genes that are relevant for cancer. We performed OncoMap v4 in formalin-fixed paraffin-embedded (FFPE) tissue specimens from 237 gastric adenocarcinomas. Using OncoMap v4, we found that 34 (14.4%) of 237 gastric cancer patients harbored mutations. Among mutations we screened, PIK3CA mutations were the most frequent (5.1%) followed by p53 (4.6%), APC (2.5%), STK11 (2.1%), CTNNB1 (1.7%), and CDKN2A (0.8%). Six samples harbored concomitant somatic mutations. Mutations of CTNNB1 were significantly more frequent in EBV-associated gastric carcinoma (P = 0.046). Our study led to the detection of potentially druggable mutations in gastric cancer which may guide novel therapies in subsets of gastric cancer patients. Conclusions/Significance Using high throughput mutation screening platform, we identified that PIK3CA mutations were the most frequently observed target for gastric adenocarcinoma.
Sound Localization Skills in Children Who Use Bilateral Cochlear Implants and in Children With Normal Acoustic Hearing

Objectives: To measure sound source localization in children who have sequential bilateral cochlear implants (BICIs); to determine whether localization accuracy correlates with performance on a right-left discrimination task (i.e., spatial acuity); to determine whether there is a measurable bilateral benefit on a sound source identification task (i.e., localization accuracy) by comparing performance under bilateral and unilateral listening conditions; and to determine whether sound source localization continues to improve with longer durations of bilateral experience. Design: Two groups of children participated in this study: a group of 21 children who received BICIs in sequential procedures (5 to 14 years) and a group of 7 typically developing children with normal acoustic hearing (5 years). Testing was conducted in a large sound-treated booth with loudspeakers positioned on a horizontal arc with a radius of 1.2 m. Children participated in two experiments that assessed spatial hearing skills. Spatial hearing acuity was assessed with a discrimination task in which listeners determined whether a sound source was presented on the right or left side of center; the smallest angle at which performance on this task was reliably above chance is the minimum audible angle. Sound localization accuracy was assessed with a sound source identification task in which children identified the perceived position of the sound source from a multiloudspeaker array (7 or 15); errors are quantified using the root mean square (RMS) error. Results: Sound localization accuracy was highly variable among the children with BICIs, with RMS errors ranging from 19 to 56°. Performance of the normal hearing group, with RMS errors ranging from 9 to 29° was significantly better. Within the BICI group, in 11 of 21 children, RMS errors were smaller in the bilateral versus unilateral listening condition, indicating bilateral benefit. There was a significant correlation between spatial acuity and sound localization accuracy (R2 = 0.68, p < 0.01), suggesting that children who achieve small RMS errors tend to have the smallest minimum audible angles. Although there was large intersubject variability, testing of 11 children in the BICI group at two sequential visits revealed a subset of children who show improvement in spatial hearing skills over time. Conclusions: A subset of children who use sequential BICIs can acquire sound localization abilities, even after long intervals between activation of hearing in the first- and second-implanted ears. This suggests that children with activation of the second implant later in life may be capable of developing spatial hearing abilities. The large variability in performance among the children with BICIs suggests that maturation of sound localization abilities in children with BICIs may be dependent on various individual subject factors such as age of implantation and chronological age.
Knowledge and awareness of the Consumer Protection Act among dental professionals in India: A systematic review

Background: The medical profession has been included in the Consumer Protection Act (CPA), to protect the interests of the patients in case of any unethical treatment rendered by the doctor. The present systematic review was conducted to assess the knowledge and awareness of CPA among dental professionals in India. Materials and Methods: A systematic review of relevant cross-sectional observational studies was conducted regarding the level of knowledge and awareness of CPA among dental professionals in India. Five studies out of 44 were finally included in the present review, after conducting both an electronic and manual search of scientific databases. The potential biases were reported and appropriate data was extracted by the concerned investigators. Results: More than 90% of the study subjects in one of the studies were aware of the CPA, as compared to other studies. In two studies, when queried about the correct time period during which a patient can sue a doctor, very few subjects (18 and 23.2%) answered correctly. Almost 90% of the subjects were taking some form of consent in one of the studies. Private practitioners had more awareness as compared to academicians and combined practitioners. Conclusion: The results of the present review showed that a majority of the subjects were aware of the existence of CPA, but knowledge about the basic rules and regulations was lacking in a few studies. Therefore, dental professionals need to keep themselves updated on the various rules and latest amendments to save themselves from any litigation.