Miracle-dz/UniFAR-FTUs huggingface dataset:
Metal‐specific control of gene expression mediated by Bradyrhizobium japonicum Mur and Escherichia coli Fur is determined by the cellular context

Bradyrhizobium japonicum Mur and Escherichia coli Fur are manganese‐ and iron‐responsive transcriptional regulators, respectively, that belong to the same protein family. Here, we show that neither Mur nor Fur discriminate between Fe2+ and Mn2+in vitro nor is there a metal preference for conferral of DNA‐binding activity on the purified proteins. When expressed in E. coli, B. japonicum Mur responded to iron, but not manganese, as determined by in vivo promoter occupancy and transcriptional repression activity. Moreover, E. coli Fur activity was manganese‐dependent in B. japonicum. Total and chelatable iron levels were higher in E. coli than in B. japonicum under identical growth conditions, and Mur responded to iron in a B. japonicum iron export mutant that accumulated high levels of the metal. However, elevated manganese content in E. coli did not confer activity on Fur or Mur, suggesting a regulatory pool of manganese in B. japonicum that is absent in E. coli. We conclude that the metal selectivity of Mur and Fur depends on the cellular context in which they function, not on intrinsic properties of the proteins. Also, the novel iron sensing mechanism found in the rhizobia may be an evolutionary adaptation to the cellular manganese status.
Targeting SIRPα in cancer

Strategies to harness the patient’s immune system to fight cancer have mainly involved adoptive T-cell transfer. We and others have recently highlighted an alternative immunotherapeutic approach to cancer that consists of enhancing the macrophage-mediated clearance of leukemia cells through the blockade of inhibitory signals transmitted by signal regulatory protein α (SIRPα).
Cell surface acetylcholinesterase molecules on multinucleated myotubes are clustered over the nucleus of origin

Multinucleated skeletal muscle fibers are compartmentalized with respect to the expression and organization of several intracellular and cell surface proteins including acetylcholinesterase (AChE). Mosaic muscle fibers formed from homozygous myoblasts expressing two allelic variants of AChE preferentially translate and assemble the polypeptides in the vicinity of the nucleus encoding the mRNA (Rotundo, R. L. 1990. J. Cell Biol. 110:715-719). To determine whether the locally synthesized AChE molecules are targeted to specific regions of the myotube surface, primary quail myoblasts were mixed with mononucleated cells of the mouse muscle C2/C12 cell line and allowed to fuse, forming heterospecific mosaic myotubes. Cell surface enzyme was localized by immunofluorescence using an avian AChE-specific monoclonal antibody. HOECHST 33342 was used to distinguish between quail and mouse nuclei in myotubes. Over 80% of the quail nuclei exhibited clusters of cell surface AChE in mosaic quail-mouse myotubes, whereas only 4% of the mouse nuclei had adjacent quail AChE-positive regions of membrane, all of which were located next to a quail nucleus. In contrast, membrane proteins such as Na+/K+ ATPase, which are not restricted to specific regions of the myotube surface, are free to diffuse over the entire length of the fiber. These studies indicate that the AChE molecules expressed in multinucleated muscle fibers are preferentially transported and localized to regions of surface membrane overlying the nucleus of origin. This targeting could play an important role in establishing and maintaining specialized cell surface domains such as the neuromuscular and myotendinous junctions.
A rare case of woolly hair with unusual associations

Woolly hair is a congenital abnormality of scalp hair manifesting as short, kinked hair, which may also involve the hair over the other parts of the body. Keratosis pilaris has been a well known association of woolly hair, and can also be a part of the Naxos or Carvajal syndromes. We herein present a case of woolly hair with associated keratosis pilaris, canaliform dystrophy of nails, increased interdental spaces and recurrent bullous impetigo. Although keratosis pilaris and teeth abnormalities have been reported as isolated associations with woolly hair, such a combination of findings as seen in our patient has not been reported before.
Self-organization of price fluctuation distribution in evolving markets

Financial markets can be seen as complex systems in non-equilibrium steady state, one of whose most important properties is the distribution of price fluctuations. Recently, there have been assertions that this distribution is qualitatively different in emerging markets as compared to developed markets. Here we analyse both high-frequency tick-by-tick as well as daily closing price data to show that the price fluctuations in the Indian stock market, one of the largest emerging markets, have a distribution that is identical to that observed for developed markets (e.g., NYSE). In particular, the cumulative distribution has a long tail described by a power law with an exponent α ≈ 3. Also, we study the historical evolution of this distribution over the period of existence of the National Stock Exchange (NSE) of India, which coincided with the rapid transformation of the Indian economy due to liberalization, and show that this power law tail has been present almost throughout. We conclude that the “inverse cubic law” is a truly universal feature of a financial market, independent of its stage of development or the condition of the underlying economy.
Renal rickets-practical approach

Rickets/osteomalacia is an important problem in a tropical country. Many cases are due to poor vitamin D intake or calcium deficient diets and can be corrected by administration of calcium and vitamin D. However, some cases are refractory to vitamin D therapy and are related to renal defects. These include rickets of renal tubular acidosis (RTA), hypophosphatemic rickets, and vitamin D dependent rickets (VDDR). The latter is due to impaired action of 1α-hydroxylase in renal tubule. These varieties need proper diagnosis and specific treatment.
Optical properties and energy parameters of Gd2O3 and Gd2O3:Er nanoparticles

The reflection spectra of Gd2O3 and Gd2O3:Er nanoparticles have been investigated. Several types of absorption centers associated with Er3+ activator ions and intrinsic lattice defects have been revealed. It was found that interband absorption is formed by indirect optical transitions with participation of phonons. The values of energy gap and phonons energy were determined.
Running user studies with crowd workers

Crowd work platforms are becoming popular among researchers in HCI and other fields for social, behavioral, and user experience studies. Platforms like Amazon Mechanical Turk (AMT) connect researchers, who set the studies up as tasks or jobs, to crowd workers recruited to complete the tasks for payment. Crowd workers on AMT (called Turkers) are quick and easy to recruit for online studies, are cheaper than paying people to come to the lab, and can provide useful feedback on prototypes through user research [1,2,3]. Plus, Turkers are considered more representative of the general (U.S.based) population than the convenient undergraduate sample prevalent in academic research [4]. But behavioral and user studies on crowd work platforms can unearth challenges foreign to more traditional user research studies. For example, Turkers don’t see themselves as study participants but rather as workers; they come to the AMT platform to do work and get paid, not to help with research. On the side of the crowd employer (called a Requester in AMT), it is easy to ignore Turkers; their work is mostly anonymous and the crowd work platform manages the labor arrangement and transactions, making it trivial to reject or even steal work [5]. A poorly designed experiment, such as a broken study platform or faulty survey questions, is difficult to detect because of the lack of direct contact between the researcher and participants. Further, such studies are often carried out quickly: A large number of workers can be recruited in a short amount of time, making it difficult to detect problems in the study until after many participants have engaged with it. Here, we report on the lessons we learned about conducting research with crowd workers while running a behavioral experiment in AMT. We discovered the gray area of being both a researcher and an employer, and learned through trial and error what it takes to be a responsible researcher dealing with a large participant crowd. We hope that other researchers interested in using crowd platforms for user studies and behavioral experiments can learn from these lessons about treating crowd participants ethically and collaborating with them toward good results for the researcher and meaningful participation for the worker.
Dust clouds or magnetic spots? Exploring the atmospheres of L dwarfs with time-resolved spectrophotometry

I present the results of a program to spectrophotometrically monitor the L1.5 dwarf 2MASSW J1145572+231730 to identify the cause of photospheric variability in ultra cool dwarfs. Plausible candidates are magnetically-induced star spots and inhomogeneous photospheric dust clouds. Based on the atmospheric models and synthetic spectra of Allard et al. (2001), the expected signatures of these phenomena in the 0.5–2.5 μ m wavelength region are presented and discussed. Near infrared spectra of 2M1145 were obtained along with a nearby reference star observed simultaneously in the spectrograph slit. No convincing variability over a 54 hour interval is found in any one of several colour indices designed to be most sensitive to dust- and spot-related variability. Nonetheless, a significant correlation between the variability of two colour indices is found. This is slightly more consistent with the dust-related variability model than the cool spot one considered. Based on the theoretically predicted signatures and the median errors in the colour indices (0.03–0.05 mag), upper limits are placed on the coverage of possible spots and clouds. Assuming the L dwarf to be best modelled by a dusty atmosphere at 1900 K, coherent clear clouds are limited to a coverage of 10–15% of the projected surface area and 200 K cooler spots to a 20% coverage. A larger coverage of many small features varying incoherently cannot be ruled out with this method. A lower effective temperature restricts coherent clear clouds to be much smaller; a higher temperature allows both clouds and spots to be larger. These upper limits are consistent with the two separate variability detections in the I -band reported by Bailer-Jones & Mundt (2001).
Generalized Minimum Bayes Risk System Combination

Minimum Bayes Risk (MBR) has been used as a decision rule for both singlesystem decoding and system combination in machine translation. For system combination, we argue that common MBR implementations are actually not correct, since probabilities in the hypothesis space cannot be reliably estimated. These implementations achieve the effect of consensus decoding (which may be beneficial in its own right), but does not reduce Bayes Risk in the true Bayesian sense. We introduce Generalized MBR, which parameterizes the loss function in MBR and allows it to be optimized in the given hypothesis space of multiple systems. This extension better approximates the true Bayes Risk decision rule and empirically improves over MBR, even in cases where the combined systems are of mixed quality.
Mining Frequent Fuzzy Grids in Dynamic Databases with Weighted Transactions and Weighted Items

Incremental mining algorithms that derive the latest mining output by making use of previous mining results are attractive to business organisations. In this paper, a fuzzy data mining algorithm for incremental mining of frequent fuzzy grids from quantitative dynamic databases is proposed. It extends the traditional association rule problem by allowing a weight to be associated with each item in a transaction and with each transaction in a database to reflect the interest/intensity of items and transactions. It uses the information about fuzzy grids that are already mined from original database and avoids start-from-scratch process. In addition, we deal with "weights-of-significance" which are automatically regulated as the incremental databases are evolved and implant themselves in the original database. We maintain "hopeful fuzzy grids" and "frequent fuzzy grids" and our algorithm changes the status of the grids which have been discovered earlier so that they reflect the pattern drift in the updated quantitative databases. Our heuristic approach avoids maintaining many "hopeful fuzzy grids" at the initial level. The algorithm is illustrated with one numerical example and demonstration of experimental results are also incorporated.
Deep Stereo Matching with Dense CRF Priors

Stereo reconstruction from rectified images has recently been revisited within the context of deep learning. Using a deep Convolutional Neural Network to obtain patch-wise matching cost volumes has resulted in state of the art stereo reconstruction on classic datasets like Middlebury and Kitti. By introducing this cost into a classical stereo pipeline, the final results are improved dramatically over non-learning based cost models. However these pipelines typically include hand engineered post processing steps to effectively regularize and clean the result. Here, we show that it is possible to take a more holistic approach by training a fully end-to-end network which directly includes regularization in the form of a densely connected Conditional Random Field (CRF) that acts as a prior on inter-pixel interactions. We demonstrate that our approach on both synthetic and real world datasets outperforms an alternative end-to-end network and compares favorably to more hand engineered approaches.
Testicular sperm aneuploidy in non-obstructive azoospermic patients.

BACKGROUND Non-obstructive azoospermic (NOA) men can father children after testicular sperm extraction (TESE). Previous studies suggest that they may be at risk of producing chromosomally abnormal spermatozoa, but the number of sperm analysed per patient was usually very low. METHODS Multicolour fluorescence in situ hybridization was used for detection of chromosome 13, 15, 16, 18, 21, 22, X and Y disomy and diploidy in sperm obtained from NOA men (n = 17) and control donors (n = 10). At least 500 testicular sperm were scored in each patient to increase the precision of our study. RESULTS The mean frequency of overall disomy (2.32%) and diploidy (0.80%) found in 13 689 testicular spermatozoa of NOA patients was significantly higher than in the ejaculated sperm of normospermic control donors, disomy (0.62%) and diploidy (0.29%). A highly significant increase in frequencies of chromosome 15, Y and overall disomy (P < 0.001), and a significant increase in disomy of chromosome 13 (P = 0.002), 16 (P = 0.031) and 21 (P = 0.018), overall diploidy (P = 0.031) and diploidy caused by errors in meiosis I (P = 0.011) were observed in the NOA group. CONCLUSIONS Testicular sperm samples of NOA patients show a higher incidence of numerical chromosomal abnormalities compared with ejaculated sperm of control donors. Appropriate genetic counselling is necessary in NOA men undergoing TESE.
Direct extracranial to intracranial bypass for stroke prevention.

tential of dysregulated signaling pathways. Indeed, miR-146 lies downstream of both the EGFR and PTEN pathways, supporting the idea that it is able to integrate information from various pathways to detect whether they are moving in a protumorigenesis direction and then counteract that trend if necessary. Given this data, it would seem that miR-146a specifically and other miRNAs generally may be an attractive target for future cancer therapies, including those directed against GBM. More broadly, Mei et al’s study further elucidates the role Notch signaling plays in cancer and reinforces the importance of understanding this critical pathway.
Mapping mHealth Research: A Decade of Evolution

Background For the last decade, mHealth has constantly expanded as a part of eHealth. Mobile applications for health have the potential to target heterogeneous audiences and address specific needs in different situations, with diverse outcomes, and to complement highly developed health care technologies. The market is rapidly evolving, making countless new mobile technologies potentially available to the health care system; however, systematic research on the impact of these technologies on health outcomes remains scarce. Objective To provide a comprehensive view of the field of mHealth research to date and to understand whether and how the new generation of smartphones has triggered research, since their introduction 5 years ago. Specifically, we focused on studies aiming to evaluate the impact of mobile phones on health, and we sought to identify the main areas of health care delivery where mobile technologies can have an impact. Methods A systematic literature review was conducted on the impact of mobile phones and smartphones in health care. Abstracts and articles were categorized using typologies that were partly adapted from existing literature and partly created inductively from publications included in the review. Results The final sample consisted of 117 articles published between 2002 and 2012. The majority of them were published in the second half of our observation period, with a clear upsurge between 2007 and 2008, when the number of articles almost doubled. The articles were published in 77 different journals, mostly from the field of medicine or technology and medicine. Although the range of health conditions addressed was very wide, a clear focus on chronic conditions was noted. The research methodology of these studies was mostly clinical trials and pilot studies, but new designs were introduced in the second half of our observation period. The size of the samples drawn to test mobile health applications also increased over time. The majority of the studies tested basic mobile phone features (eg, text messaging), while only a few assessed the impact of smartphone apps. Regarding the investigated outcomes, we observed a shift from assessment of the technology itself to assessment of its impact. The outcome measures used in the studies were mostly clinical, including both self-reported and objective measures. Conclusions Research interest in mHealth is growing, together with an increasing complexity in research designs and aim specifications, as well as a diversification of the impact areas. However, new opportunities offered by new mobile technologies do not seem to have been explored thus far. Mapping the evolution of the field allows a better understanding of its strengths and weaknesses and can inform future developments.
Atrial fibrillation and risk.

Dr. Camm received an honorarium through an educational grant from Sanofi Aventis to serve as Guest Editor of this supplement. He discloses no other direct conflicts of interest to the submitted work. Dr. Camm has served as a consultant, received grant funding, and has been a member of the speakers bureau for Sanofi Aventis.
Transfer of fetal cells with multilineage potential to maternal tissue.

CONTEXT During pregnancy, fetal CD34+ cells enter the maternal circulation, persist for decades, and create a state of physiologic microchimerism. Many studies have confirmed the residual presence of fetal cells in maternal blood and tissues following pregnancy. Fetal cells may respond to maternal injury by developing multilineage capacity in maternal organs. OBJECTIVE To verify that fetal microchimeric cells express markers of epithelial, leukocyte, and hepatocyte differentiation within maternal organs. DESIGN, SETTING, AND PATIENTS Archived paraffin-embedded tissue section specimens from 10 women who had male offspring and were previously found to have high numbers of microchimeric cells, and 11 control women who had no prior male pregnancies. Male cells were identified by fluorescence in situ hybridization, using X and Y chromosome-specific probes, followed by histologic and immunochemical studies using anticytokeratin (AE1/AE3) as a marker of epithelial cells, anti-CD45 as a leukocyte marker, and heppar-1 as a hepatocyte marker. MAIN OUTCOME MEASURE Percentage of microchimeric cells expressing nonhematopoietic markers. RESULTS A total of 701 male (XY+) microchimeric cells were identified (mean [SD], 227 [128] XY+ cells per million maternal cells). In maternal epithelial tissues (thyroid, cervix, intestine, and gallbladder), 14% to 60% of XY+ cells expressed cytokeratin. Conversely, in hematopoietic tissues, such as lymph nodes and spleen, 90% of XY+ cells expressed CD45. In 1 liver sample, 4% of XY+ cells expressed heppar-1. Histologic and immunochemical evidence of differentiation, as assessed by independent observers, was highly concordant (kappa = 0.72). CONCLUSION The detection of microchimeric male cells, bearing epithelial, leukocyte, or hepatocyte markers, in a variety of maternal tissue specimens suggests the presence of fetal cells that may have multilineage capacity.
Ultrasound Biomicroscopy in Narrow Peripheral Anterior Chamber Eyes With or Without Peripheral Anterior Synechiae

AimTo compare the configurations of the anterior ocular segment including the anterior chamber (AC) angle and ciliary body between eyes with a narrow AC angle (ACA) with and without peripheral anterior synechiae (PAS). Patients and MethodsOne hundred and one eyes of 101 consecutive patients with a temporal peripheral AC depth one-quarter of the corneal thickness or less were included. Gonioscopy and ultrasound biomicroscopy were performed under light and dark conditions. The existence of PAS was further confirmed with compression gonioscopy with indentation. Eyes with findings suggestive of plateau iris configuration or those with glaucomatous optic neuropathy were carefully excluded. The biometric parameters including the ACA, the angle opening distance at 500 μm, the trabecular-ciliary process distance, the iris-zonule distance, and the scleral-ciliary process angle were determined. ResultsPAS were found in 43 (43%) of the 101 eyes. There were no differences in age, refractive error, or intraocular pressure between PAS-positive and PAS-negative eyes (P>0.1). ACA, iris-zonule distance, scleral-ciliary process angle under light and/or dark conditions were significantly smaller in the PAS-positive eyes than in the PAS-negative eyes (P<0.05). ConclusionsShallow peripheral AC depth and relatively anteriorly located ciliary body was significantly associated with the presence of PAS in eyes with a narrow ACA.